@sackville-mcp/mutate 0.0.1-alpha.3 → 0.0.1-alpha.4

package/dist/index.d.mts

@@ -1,3 +1,5 @@
+import { SpawnedRunner } from "@sackville-mcp/spawn";
+
 //#region src/config.d.ts
 /**
  * Diff-scoping config EMITTERS for the Python mutation tools (ADR 0010 addendum 2). These turn a
@@ -217,14 +219,7 @@ interface RunMutationInput {
   ownedRoots?: string[];
 }
 /** Injected command runner — executes `stryker <argv>` and yields its exit status. */
-type MutationRunner = (argv: string[], opts: {
-  cwd: string;
-  timeoutMs?: number;
-}) => Promise<{
-  exitCode: number;
-  stdout: string;
-  stderr: string;
-}>;
+type MutationRunner = SpawnedRunner;
 interface RunMutationResult {
   ran: boolean;
   exitCode: number;

package/dist/index.d.mts.map

@@ -1 +1 @@
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+{"version":3,"file":"index.d.mts","names":[],"sources":["../src/config.ts","../src/summarize.ts","../src/cosmic-ray.ts","../src/mutmut.ts","../src/run.ts","../src/scope.ts"],"mappings":";;;;;;AAsBA;;;;;;;;AAC6B;AAkE7B;;;;AAAsD;AAUtD;;cA7Ea,cAAA,SAAuB,KAAK;cAC3B,OAAA;AAAA;;;;AAkFM;AAUpB;iBA1BgB,qBAAA,CAAsB,QAAgB;AAAA,UAUrC,qBAAA;EAmBO;EAjBtB,IAAA;EAgBA;EAdA,UAAA;EAesB;EAbtB,kBAAA;AAAA;;;;AAqDuD;AAMzD;;;iBAjDgB,+BAAA,CACd,QAAA,UACA,aAAA,aACC,qBAAqB;AA8C+B;AAAA,iBANvC,mBAAA,CAAoB,aAAqB;;iBAMzC,iBAAA,CAAkB,aAAqB;AAAA,UAKtC,eAAA;EAEf;EAAA,aAAA;EAIA;EAFA,QAAA;EAImB;EAFnB,WAAA;EAYc;EAVd,mBAAA;AAAA;;;;;;;AAcgB;iBAJF,eAAA,CACd,aAAA,YACA,cAAA,YACA,oBAAA,cACC,eAAe;;;;;;;;iBA0BF,+BAAA,CACd,aAAA,UACA,IAAA,EAAM,eAAe;;;;;;AArMvB;;;;;;;;AAC6B;AAkE7B;;;;AAAsD;AAUtD;;;;;;;;AAMoB;AAUpB;;KCtFY,YAAA;AAAA,UAUK,cAAA;EACf,IAAA;EACA,MAAM;AAAA;AAAA,UAGS,MAAA;EACf,EAAA;EACA,WAAA;EACA,MAAA,EAAQ,YAAA;EACR,WAAA;EACA,QAAA;IAAa,KAAA,EAAO,cAAA;IAAgB,GAAA,GAAM,cAAA;EAAA;AAAA;AAAA,UAG3B,YAAA;EACf,QAAA;EACA,MAAA;EACA,OAAA,EAAS,MAAM;AAAA;AAAA,UAGA,cAAA;EACf,aAAA;EACA,UAAA;IAAe,IAAA;IAAc,GAAA;EAAA;EAC7B,KAAA,EAAO,MAAM,SAAS,YAAA;AAAA;AAAA,UAGP,YAAA;EACf,MAAA;EACA,QAAA;EACA,OAAA;EACA,UAAA;EACA,aAAA;EACA,aAAA;EACA,OAAA;EACA,OAAA;AAAA;AAAA,UAGe,eAAA;EACf,MAAA,EAAQ,YAAY;EACpB,QAAA;EACA,UAAA;EACA,OAAA;EACA,KAAA;EACA,OAAA;EACA,YAAA;;EAEA,aAAA;;EAEA,+BAAA;AAAA;AAAA,UAGe,WAAA;EACf,IAAA;EACA,OAAA,EAAS,eAAe;AAAA;;UAIT,QAAA;EACf,IAAA;EACA,WAAA;EACA,MAAA;EACA,IAAA;AAAA;AAAA,UAGe,eAAA;EACf,OAAA,EAAS,eAAA;EACT,KAAA,EAAO,WAAA;EAvDiD;EAyDxD,SAAA,EAAW,QAAA;AAAA;;iBAiFG,iBAAA,CAAkB,MAAA,EAAQ,cAAA,GAAiB,eAAe;;;ADxE1E;AAAA,iBE3CgB,kBAAA,CAAmB,KAAA,WAAgB,cAAc;;;;iBC5BjD,kBAAA,CAAmB,IAAA,WAAe,cAAc;;;;cCiDnD,eAAA,SAAwB,KAAK;cAC5B,OAAA;AAAA;AAAA,UAWG,iBAAA;EJU8B;EIR7C,WAAA;EJWsB;EITtB,YAAA;EJQA;EINA,QAAA;EJOsB;EILtB,SAAA;AAAA;AAAA,UAGe,gBAAA;;;AJ0CwC;AAMzD;;;EIzCE,WAAA;EJyCqD;EIvCrD,WAAA;EJ4C8B;EI1C9B,UAAA;EJ0C8B;;;;;EIpC9B,UAAA;AAAA;AJsDF;AAAA,KIlDY,cAAA,GAAiB,aAAa;AAAA,UAEzB,iBAAA;EACf,GAAA;EACA,QAAA;EJgDA;EI9CA,WAAA;EJgDC;EI9CD,IAAA;EJ8CgB;AA0BlB;;;EInEE,UAAA;EACA,OAAA,EAAS,eAAe;EJoElB;EIlEN,UAAA;EJkEqB;EIhErB,SAAA;;EAEA,cAAA;AAAA;AHhIF;AAAA,cGmJa,oBAAA,EAAsB,cAAuC;;cAG7D,mBAAA,EAAqB,cAAsC;AHtJhD;AAAA,cGyJX,sBAAA,EAAwB,cAA0C;;;;AH7IvE;AAGR;;iBG6JsB,WAAA,CACpB,MAAA,EAAQ,iBAAA,EACR,KAAA,EAAO,gBAAA,EACP,IAAA;EAAQ,MAAA,GAAS,cAAA;EAAgB,UAAA;AAAA,IAChC,OAAA,CAAQ,iBAAA;;;;;;;iBAwDW,SAAA,CACpB,MAAA,EAAQ,iBAAA,EACR,KAAA,EAAO,gBAAA,EACP,IAAA;EACE,MAAA,GAAS,cAAA,EHxNE;EG0NX,MAAA,IAAU,IAAA,sBH1NwB;EG4NlC,eAAA,IAAmB,UAAA,YAAsB,WAAA,uBH5Na;EG8NtD,UAAA;AAAA,IAED,OAAA,CAAQ,iBAAA;;;;;;;;;AH1NM;iBG6SK,YAAA,CACpB,MAAA,EAAQ,iBAAA,EACR,KAAA,EAAO,gBAAA,EACP,IAAA;EACE,MAAA,GAAS,cAAA;EACT,UAAA,WH5SW;EG8SX,MAAA,IAAU,IAAA,sBH/SZ;EGiTE,gBAAA;AAAA,IAED,OAAA,CAAQ,iBAAA;;;UCtVM,aAAA;;EAEf,KAAA;EL0EA;;EKvEA,SAAS;AAAA;AL2ES;AAUpB;;;;;;;;AAVoB,iBK/DJ,mBAAA,CACd,WAAA,YACA,UAAA,YACA,MAAA,GAAS,IAAA,uBACR,aAAa;AAAA,UAiBC,mBAAA;EL+FkB;;EK5FjC,YAAA;EL4FuD;AAMzD;EK/FE,OAAO;AAAA;;AL+F8C;AAKvD;;;;;;;iBKxFgB,cAAA,CAAe,QAAA,YAAoB,OAAA,EAAS,eAAA,GAAkB,mBAAmB;;ALgG5E;AAUrB;;;;iBKxFgB,cAAA,CAAe,IAAY;;;;;AL4FzB;AA0BlB;;;;iBKvGgB,oBAAA,CACd,aAAA,YACA,OAAA,EAAS,eAAA,GACR,mBAAmB"}

package/dist/index.mjs

@@ -1,8 +1,8 @@
 import { parse, stringify } from "smol-toml";
-import { execFile } from "node:child_process";
 import { cpSync, existsSync, mkdtempSync, readFileSync, readdirSync, rmSync, writeFileSync } from "node:fs";
 import { tmpdir } from "node:os";
 import { join, resolve } from "node:path";
+import { spawnRunner } from "@sackville-mcp/spawn";
 //#region src/config.ts
 /**
 * Diff-scoping config EMITTERS for the Python mutation tools (ADR 0010 addendum 2). These turn a
@@ -559,28 +559,12 @@ function runArgv(input) {
 	if (input.incremental) argv.push("--incremental");
 	return argv;
 }
-/** Spawn a local command as a subprocess, surfacing its exit code (never rejecting on non-zero). */
-function spawnMutationRunner(command) {
-	return (argv, opts) => new Promise((res) => {
-		execFile(command, argv, {
-			cwd: opts.cwd,
-			timeout: opts.timeoutMs,
-			maxBuffer: 64 * 1024 * 1024
-		}, (err, stdout, stderr) => {
-			res({
-				exitCode: err && typeof err.code === "number" ? err.code : err ? 1 : 0,
-				stdout: String(stdout),
-				stderr: String(stderr)
-			});
-		});
-	});
-}
 /** Default live runner: spawn the local `stryker` as a subprocess (used by the bin, not the gate). */
-const defaultStrykerRunner = spawnMutationRunner("stryker");
+const defaultStrykerRunner = spawnRunner("stryker");
 /** Default live runner: spawn the local `mutmut` as a subprocess (used by the bin, not the gate). */
-const defaultMutmutRunner = spawnMutationRunner("mutmut");
+const defaultMutmutRunner = spawnRunner("mutmut");
 /** Default live runner: spawn the local `cosmic-ray` as a subprocess (used by the bin, not the gate). */
-const defaultCosmicRayRunner = spawnMutationRunner("cosmic-ray");
+const defaultCosmicRayRunner = spawnRunner("cosmic-ray");
 function assertAllowed(config) {
 	if (!config.allowRun) throw new MutateGateError("mutation runs are not enabled (the operator must set allowRun)");
 	const root = resolve(config.projectRoot);

package/dist/index.mjs.map

@@ -1 +1 @@
-{"version":3,"file":"index.mjs","names":["normalizePath"],"sources":["../src/config.ts","../src/cosmic-ray.ts","../src/mutmut.ts","../src/scope.ts","../src/summarize.ts","../src/run.ts"],"sourcesContent":["/**\n * Diff-scoping config EMITTERS for the Python mutation tools (ADR 0010 addendum 2). These turn a\n * selected-file scope into a per-run tool config, PINNED to the slice-0 captures of the installed\n * cosmic-ray 8.4.6 / mutmut 3.5.0 (see `test/fixtures/README.md`) — never doc-derived guesses:\n *\n * - cosmic-ray scopes via a `module-path` FILE LIST (Fork A — verified 8.4.6 accepts a list); its\n *   `excluded-modules` SUBTRACTS from the scope via exact path AND fnmatch glob, so an inherited\n *   exclusion that matches a selected file is reconciled (stripped), never copied blind (blocker #3).\n * - mutmut scopes via `paths_to_mutate` (Fork B was WRONG — 3.5.0 has NO `only_mutate`/`source_paths`;\n *   `paths_to_mutate` + `do_not_mutate` are the real keys, Fork F). Scoping a subset breaks the\n *   baseline unless the rest of the source tree is `also_copy`'d so unscoped tests still import; an\n *   inherited `do_not_mutate` glob matching a selected file is stripped (blocker #3, mutmut form).\n *\n * Both emitters are PURE (TOML in → TOML out via `smol-toml`). They reduce SPURIOUS inconclusives by\n * reconciling exclusions up front; the load-bearing under-scope guarantee is the POST-SPAWN\n * {@link reconcileScope} guard in the runner, which folds any genuinely-unmutated selected file to\n * inconclusive regardless of why (absence-is-never-a-pass).\n */\n\nimport { parse, stringify } from 'smol-toml'\n\n/** Thrown when a scoped config cannot be safely synthesized (empty scope, missing base table, etc.). */\nexport class ScopeEmitError extends Error {\n  constructor(message: string) {\n    super(message)\n    this.name = 'ScopeEmitError'\n  }\n}\n\n/** Normalize a path to a comparable repo-relative POSIX form (backslashes → `/`, drop a leading `./`). */\nfunction normalizePath(p: string): string {\n  return p.replace(/\\\\/g, '/').replace(/^\\.\\//, '')\n}\n\n/** Dedupe + normalize + sort, the canonical scope form used everywhere. */\nfunction canonicalize(paths: string[]): string[] {\n  return [...new Set(paths.map(normalizePath))].sort()\n}\n\n/**\n * Translate a Python `fnmatch` pattern to an anchored RegExp. Mirrors `fnmatch.translate`: a star →\n * `.*` (crosses `/`, unlike shell glob — so a `star + /strutil.py` glob matches `pkg/strutil.py`),\n * `?` → any one char, `[seq]`/`[!seq]` → char class, everything else escaped. This is the matcher\n * cosmic-ray's `excluded-modules` and mutmut's `do_not_mutate` both use (the latter via\n * `fnmatch.fnmatch` in `Config.should_ignore_for_mutation`).\n */\nfunction fnmatchToRegExp(pattern: string): RegExp {\n  let re = ''\n  let i = 0\n  const n = pattern.length\n  while (i < n) {\n    const c = pattern[i++]\n    if (c === '*') {\n      re += '.*'\n    } else if (c === '?') {\n      re += '.'\n    } else if (c === '[') {\n      let j = i\n      if (j < n && (pattern[j] === '!' || pattern[j] === ']')) j++\n      while (j < n && pattern[j] !== ']') j++\n      if (j >= n) {\n        re += '\\\\[' // unterminated class → literal '['\n      } else {\n        let stuff = pattern.slice(i, j).replace(/\\\\/g, '\\\\\\\\')\n        i = j + 1\n        if (stuff.startsWith('!')) stuff = `^${stuff.slice(1)}`\n        else if (stuff.startsWith('^')) stuff = `\\\\${stuff}`\n        re += `[${stuff}]`\n      }\n    } else {\n      re += (c ?? '').replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\$&')\n    }\n  }\n  return new RegExp(`^(?:${re})$`, 's')\n}\n\n/** True if an exclusion entry (exact path or fnmatch glob) matches any of the selected files. */\nfunction exclusionCollides(entry: string, selected: string[]): boolean {\n  const norm = normalizePath(entry)\n  if (selected.includes(norm)) return true // exact path\n  const re = fnmatchToRegExp(norm)\n  return selected.some((f) => re.test(f))\n}\n\n/**\n * The operator's declared source tree, read from a cosmic-ray base config's `module-path` (a single\n * string or a list). Used as the default `ownedRoots` to confine the diff scope (Fork C): a changed\n * `.py` outside this tree is `unmatched` (report-gap), never silently scoped. Pure.\n */\nexport function cosmicModulePathRoots(baseToml: string): string[] {\n  const data = parse(baseToml) as Record<string, unknown>\n  const cr = data['cosmic-ray']\n  if (!cr || typeof cr !== 'object') return []\n  const mp = (cr as Record<string, unknown>)['module-path']\n  if (typeof mp === 'string') return [normalizePath(mp)]\n  if (Array.isArray(mp)) return mp.map((x) => normalizePath(String(x)))\n  return []\n}\n\nexport interface ScopedCosmicRayConfig {\n  /** The synthesized per-run `cosmic-ray.toml` text. */\n  toml: string\n  /** The selected file list written to `module-path` (canonical form). */\n  modulePath: string[]\n  /** Inherited `excluded-modules` entries removed because they would subtract a selected file. */\n  strippedExclusions: string[]\n}\n\n/**\n * Synthesize a per-run cosmic-ray config from a base config + the selected files. Overrides\n * `module-path` to the canonical selected FILE LIST and reconciles `excluded-modules`: any entry\n * (exact or fnmatch glob) that matches a selected file is stripped (it would otherwise silently\n * subtract that file — blocker #3); non-colliding entries are preserved. All other keys/tables\n * (`timeout`, `test-command`, `[cosmic-ray.distributor]`, …) are preserved verbatim. Pure.\n */\nexport function synthesizeScopedCosmicRayConfig(\n  baseToml: string,\n  selectedFiles: string[],\n): ScopedCosmicRayConfig {\n  const selected = canonicalize(selectedFiles)\n  if (selected.length === 0) {\n    throw new ScopeEmitError('cannot synthesize a scoped cosmic-ray config for an empty selection')\n  }\n  const data = parse(baseToml) as Record<string, unknown>\n  const cr = data['cosmic-ray']\n  if (cr === undefined || typeof cr !== 'object') {\n    throw new ScopeEmitError('base config has no [cosmic-ray] table')\n  }\n  const table = cr as Record<string, unknown>\n  table['module-path'] = selected\n\n  const strippedExclusions: string[] = []\n  const inherited = Array.isArray(table['excluded-modules'])\n    ? (table['excluded-modules'] as unknown[]).map(String)\n    : []\n  const kept = inherited.filter((entry) => {\n    if (exclusionCollides(entry, selected)) {\n      strippedExclusions.push(entry)\n      return false\n    }\n    return true\n  })\n  table['excluded-modules'] = kept\n\n  return { toml: stringify(data), modulePath: selected, strippedExclusions }\n}\n\n/** The `[tool.mutmut]` table of a pyproject (empty when absent / unparseable-as-table). */\nfunction mutmutTable(basePyproject: string): Record<string, unknown> {\n  if (!basePyproject.trim()) return {}\n  const data = parse(basePyproject) as Record<string, unknown>\n  const tool = data.tool\n  if (!tool || typeof tool !== 'object') return {}\n  const m = (tool as Record<string, unknown>).mutmut\n  return m && typeof m === 'object' ? (m as Record<string, unknown>) : {}\n}\n\n/** The operator's `[tool.mutmut] paths_to_mutate` — the default `ownedRoots` for a scoped mutmut run. */\nexport function mutmutPathsToMutate(basePyproject: string): string[] {\n  const v = mutmutTable(basePyproject).paths_to_mutate\n  return Array.isArray(v) ? v.map((x) => normalizePath(String(x))) : []\n}\n\n/** The operator's inherited `[tool.mutmut] do_not_mutate` globs (reconciled against the scope). */\nexport function mutmutDoNotMutate(basePyproject: string): string[] {\n  const v = mutmutTable(basePyproject).do_not_mutate\n  return Array.isArray(v) ? v.map(String) : []\n}\n\nexport interface MutmutScopePlan {\n  /** The selected files written to `paths_to_mutate` (canonical form). */\n  pathsToMutate: string[]\n  /** Sibling source files to `also_copy` so unscoped tests still import (source tree minus scope). */\n  alsoCopy: string[]\n  /** Inherited `do_not_mutate` globs preserved (those that do NOT collide with the scope). */\n  doNotMutate: string[]\n  /** Inherited `do_not_mutate` globs removed because they would exclude a selected file (blocker #3). */\n  strippedDoNotMutate: string[]\n}\n\n/**\n * Plan a scoped mutmut run. `paths_to_mutate` = the selected files; `also_copy` = every other source\n * file in `allSourceFiles` (so a test importing an unscoped sibling module still resolves in mutmut's\n * `mutants/` sandbox — verified necessary in slice 0). An inherited `do_not_mutate` glob that matches\n * a selected file is stripped (it would otherwise exclude a file we deliberately scoped). Pure given\n * `allSourceFiles` (the runner derives it by walking the owned roots).\n */\nexport function planMutmutScope(\n  selectedFiles: string[],\n  allSourceFiles: string[],\n  inheritedDoNotMutate: string[] = [],\n): MutmutScopePlan {\n  const pathsToMutate = canonicalize(selectedFiles)\n  if (pathsToMutate.length === 0) {\n    throw new ScopeEmitError('cannot plan a scoped mutmut run for an empty selection')\n  }\n  const scope = new Set(pathsToMutate)\n  const alsoCopy = canonicalize(allSourceFiles).filter((f) => !scope.has(f))\n\n  const strippedDoNotMutate: string[] = []\n  const doNotMutate = inheritedDoNotMutate.filter((entry) => {\n    if (exclusionCollides(entry, pathsToMutate)) {\n      strippedDoNotMutate.push(entry)\n      return false\n    }\n    return true\n  })\n  return { pathsToMutate, alsoCopy, doNotMutate, strippedDoNotMutate }\n}\n\n/**\n * Render a `pyproject.toml` for a scoped mutmut run: merge the {@link MutmutScopePlan}'s\n * `paths_to_mutate`/`also_copy` (+ reconciled `do_not_mutate`) into the base pyproject's\n * `[tool.mutmut]` table (Fork F: only slice-0-verified keys), preserving every other section and any\n * other verified `[tool.mutmut]` key the operator set (e.g. `pytest_add_cli_args`). An empty\n * `do_not_mutate` is omitted entirely. Pure.\n */\nexport function synthesizeScopedMutmutPyproject(\n  basePyproject: string,\n  plan: MutmutScopePlan,\n): string {\n  const data = (basePyproject.trim() ? parse(basePyproject) : {}) as Record<string, unknown>\n  const tool = (data.tool && typeof data.tool === 'object' ? data.tool : {}) as Record<\n    string,\n    unknown\n  >\n  const mutmut = (tool.mutmut && typeof tool.mutmut === 'object' ? tool.mutmut : {}) as Record<\n    string,\n    unknown\n  >\n  mutmut.paths_to_mutate = plan.pathsToMutate\n  mutmut.also_copy = plan.alsoCopy\n  if (plan.doNotMutate.length > 0) mutmut.do_not_mutate = plan.doNotMutate\n  else delete mutmut.do_not_mutate\n  tool.mutmut = mutmut\n  data.tool = tool\n  return stringify(data)\n}\n","/**\n * cosmic-ray adapter (a Python mutation-testing tool) — converts `cosmic-ray dump <session.sqlite>`\n * JSON-lines into the mutation-testing-elements {@link MutationReport} that {@link summarizeMutation}\n * already consumes, so the summarizer is reused unchanged across Stryker (JS), mutmut, and cosmic-ray.\n *\n * Unlike mutmut, cosmic-ray's dump carries the REAL source path + line + operator per mutant, so its\n * survivors are actionable (file:line:operator). Each dump line is a JSON array\n * `[work_item, work_result | null]` (captured from cosmic-ray 8.4.6 — see\n * `test/fixtures/cosmic-ray-dump.jsonl`):\n *\n *   - `work_item.mutations[]` — one entry per mutation in the job (single-mutation jobs in practice);\n *     each has `module_path` (the file key), `operator_name` (the mutator), and `start_pos: [line, col]`.\n *   - `work_result` — `{ worker_outcome, test_outcome? }`, or `null` when the job has not been executed.\n *\n * Status mapping (cosmic-ray → mutation-testing-elements), chosen to never overstate the score and to\n * fold ambiguity to a neutral `Pending` (never `Survived`/`Killed`):\n *   - `work_result === null`               → Pending (not yet executed)\n *   - worker_outcome `normal` + test_outcome `killed`/`survived` → Killed / Survived\n *   - worker_outcome `normal` + test_outcome `incompetent`       → RuntimeError (the mutant broke the run)\n *   - worker_outcome `no_test`             → NoCoverage (no test exercised the mutation)\n *   - worker_outcome `skipped`             → Ignored\n *   - worker_outcome `exception`/`abnormal`→ RuntimeError (invalid — excluded from the score)\n *   - worker_outcome `timeout`             → Timeout\n *   - anything else / missing test_outcome → Pending (ambiguity ⇒ neutral, never a phantom survivor)\n */\n\nimport type { Mutant, MutantStatus, MutationFile, MutationReport } from './summarize.js'\n\ninterface CosmicMutation {\n  module_path?: string\n  operator_name?: string\n  start_pos?: [number, number] | { line?: number; column?: number }\n}\ninterface CosmicWorkItem {\n  mutations?: CosmicMutation[]\n}\ninterface CosmicWorkResult {\n  worker_outcome?: string\n  test_outcome?: string | null\n}\n\n/** worker_outcome (other than `normal`) → status. `normal` defers to test_outcome. */\nconst WORKER_STATUS: Record<string, MutantStatus> = {\n  no_test: 'NoCoverage',\n  skipped: 'Ignored',\n  exception: 'RuntimeError',\n  abnormal: 'RuntimeError',\n  timeout: 'Timeout',\n}\n/** test_outcome (when worker_outcome === 'normal') → status. */\nconst TEST_STATUS: Record<string, MutantStatus> = {\n  killed: 'Killed',\n  survived: 'Survived',\n  incompetent: 'RuntimeError',\n}\n\nfunction statusOf(result: CosmicWorkResult | null): MutantStatus {\n  if (result === null) return 'Pending' // not yet executed\n  const worker = result.worker_outcome\n  if (worker === 'normal') return TEST_STATUS[result.test_outcome ?? ''] ?? 'Pending'\n  return (worker !== undefined && WORKER_STATUS[worker]) || 'Pending'\n}\n\nfunction lineColOf(\n  pos: CosmicMutation['start_pos'],\n): { line: number; column?: number } | undefined {\n  if (Array.isArray(pos)) return { line: pos[0], column: pos[1] }\n  if (pos && typeof pos.line === 'number') return { line: pos.line, column: pos.column }\n  return undefined\n}\n\n/** Parse `cosmic-ray dump <session.sqlite>` JSON-lines into a mutation-testing-elements report. Pure. */\nexport function parseCosmicRayDump(jsonl: string): MutationReport {\n  const files: Record<string, MutationFile> = {}\n  let index = 0\n  for (const raw of jsonl.split(/\\r?\\n/)) {\n    const line = raw.trim()\n    if (!line) continue\n    let parsed: [CosmicWorkItem, CosmicWorkResult | null]\n    try {\n      parsed = JSON.parse(line) as [CosmicWorkItem, CosmicWorkResult | null]\n    } catch {\n      continue // a non-JSON line (e.g. a stray log) is skipped, never a phantom mutant\n    }\n    const [workItem, workResult] = parsed\n    const mutation = workItem?.mutations?.[0]\n    const path = mutation?.module_path\n    if (!path) continue\n    const status = statusOf(workResult ?? null)\n    const loc = lineColOf(mutation.start_pos)\n    const mutant: Mutant = {\n      id: `${path}:${index}`,\n      mutatorName: mutation.operator_name ?? 'unknown',\n      status,\n    }\n    if (loc) mutant.location = { start: loc }\n    const entry = files[path] ?? { language: 'python', mutants: [] }\n    entry.mutants.push(mutant)\n    files[path] = entry\n    index++\n  }\n  return { files }\n}\n","/**\n * mutmut adapter (the Python mutation-testing tool) — converts `mutmut results --all true`\n * output into the mutation-testing-elements {@link MutationReport} that {@link summarizeMutation}\n * already consumes, so the summarizer is reused unchanged across Stryker (JS) and mutmut (Python).\n *\n * mutmut 3.x has no native mutation-testing-elements / JSON-per-mutant report; its richest\n * machine-readable per-mutant output is `mutmut results --all true`, one line per mutant:\n *\n *     calc.x_add__mutmut_1: killed\n *     calc.x_sub__mutmut_1: survived\n *     calc.x_mul__mutmut_1: no tests\n *\n * (Captured from mutmut 3.5.0 — see `test/fixtures/mutmut-results.txt`.) The mutant name is\n * `<dotted module>.x_<function>__mutmut_<n>`, so we group mutants by their module as the \"file\"\n * key (mutmut does not surface a source path or line here — `line` is 0, `mutatorName` is the\n * mutant name, the best identifier available).\n *\n * Status vocabulary mapping (mutmut → mutation-testing-elements), chosen to never overstate the\n * score: `suspicious` (the suite behaved oddly — not a confirmed kill) maps to `Survived` so it\n * surfaces as a gap; `segfault` maps to `RuntimeError` (invalid, excluded from the score); an\n * unrecognized status maps to `Pending` (neutral — excluded from `valid`, not a survivor).\n */\n\nimport type { MutantStatus, MutationFile, MutationReport } from './summarize.js'\n\nconst MUTMUT_STATUS: Record<string, MutantStatus> = {\n  killed: 'Killed',\n  survived: 'Survived',\n  'no tests': 'NoCoverage',\n  timeout: 'Timeout',\n  suspicious: 'Survived',\n  skipped: 'Ignored',\n  segfault: 'RuntimeError',\n}\n\n/** The module portion of a mutmut mutant name (`pkg.mod.x_fn__mutmut_3` → `pkg.mod`). */\nfunction moduleOf(name: string): string {\n  const m = /^(.*)\\.x_.+__mutmut_\\d+$/.exec(name)\n  if (m?.[1]) return m[1]\n  const dot = name.lastIndexOf('.')\n  return dot > 0 ? name.slice(0, dot) : name\n}\n\n/** Parse `mutmut results --all true` text into a mutation-testing-elements report. Pure. */\nexport function parseMutmutResults(text: string): MutationReport {\n  const files: Record<string, MutationFile> = {}\n  for (const raw of text.split(/\\r?\\n/)) {\n    const line = raw.trim()\n    if (!line) continue\n    const idx = line.indexOf(':')\n    if (idx === -1) continue\n    const name = line.slice(0, idx).trim()\n    if (!name) continue\n    const statusText = line\n      .slice(idx + 1)\n      .trim()\n      .toLowerCase()\n    const status = MUTMUT_STATUS[statusText] ?? 'Pending'\n    const file = moduleOf(name)\n    const entry = files[file] ?? { mutants: [] }\n    entry.mutants.push({ id: name, mutatorName: name, status })\n    files[file] = entry\n  }\n  return { files }\n}\n","/**\n * Pure scope-selection + post-spawn reconciliation primitives for Python mutation diff-scoping\n * (ADR 0010 addendum 2). The config EMITTERS (cosmic-ray TOML / mutmut pyproject) and the runner\n * wiring are STAGED pending slice-0 tool-fact capture; these two functions are the load-bearing,\n * tool-agnostic SAFETY core and ship first (pure, fixture-tested, no real tool in `pnpm gate`):\n *\n * - {@link selectMutationScope} mirrors coverage's `selectPytestScope` (incl. its INJECTED\n *   existence predicate): turn the changed-file list into the set of mutable, existing, in-tree\n *   `.py` files to scope a mutation run to, surfacing everything else as `unmatched` (report-gap;\n *   never silently folded into the scope).\n * - {@link reconcileScope} is the POST-SPAWN partial-under-scope guard (the design's load-bearing\n *   correction): the existing `assertComplete` only catches TOTAL-zero mutants, so it is blind to\n *   a run that mutated only a SUBSET of the selected files — a clean score for files that were\n *   never mutated, i.e. absence-as-a-pass. reconcileScope reports which selected files the tool\n *   actually mutated and which it NEVER SAW; the (staged) runner throws ⇒ inconclusive on any\n *   never-seen selected file.\n */\n\nimport type { MutationSummary } from './summarize.js'\n\n/** Normalize a path to a comparable repo-relative POSIX form (backslashes → `/`, drop a leading `./`). */\nfunction normalizePath(p: string): string {\n  return p.replace(/\\\\/g, '/').replace(/^\\.\\//, '')\n}\n\nexport interface MutationScope {\n  /** Mutable, existing, in-tree `.py` files to scope the run to (repo-relative, normalized, deduped, sorted). */\n  files: string[]\n  /** Changed `.py` files that are out-of-tree, deleted, or otherwise unplaceable — surfaced as a\n   * gap (report-gap), NEVER silently folded into `files` (that would be absence-as-a-pass). */\n  unmatched: string[]\n}\n\n/**\n * Derive the mutation scope from the changed files. A changed file is selected only when it is a\n * `.py` file, lives under one of the operator's `ownedRoots`, AND exists on disk (`exists`,\n * injected — FS by default in the runner, faked in tests, mirroring `selectPytestScope`'s\n * `testExists`). A `.py` file that is out-of-tree or non-existent (deleted/renamed/typo) is\n * `unmatched`, never scoped. Non-`.py` files are irrelevant to mutation and dropped. Pure given\n * `exists`. Whole-project fallback is NOT decided here — it is the caller's (`mutateFiles ===\n * undefined`) or the cosmic-ray emitter's (`no-scope` on the base config) concern.\n */\nexport function selectMutationScope(\n  mutateFiles: string[],\n  ownedRoots: string[],\n  exists: (path: string) => boolean,\n): MutationScope {\n  const roots = ownedRoots.map(normalizePath)\n  const underRoot = (p: string): boolean => roots.some((r) => p === r || p.startsWith(`${r}/`))\n  const files = new Set<string>()\n  const unmatched = new Set<string>()\n  for (const raw of mutateFiles) {\n    const p = normalizePath(raw)\n    if (!p.endsWith('.py')) continue // not a Python source file — irrelevant to mutation\n    if (!underRoot(p) || !exists(p)) {\n      unmatched.add(p) // out-of-tree, deleted, renamed, or typo'd — a gap, never scoped\n      continue\n    }\n    files.add(p)\n  }\n  return { files: [...files].sort(), unmatched: [...unmatched].sort() }\n}\n\nexport interface ScopeReconciliation {\n  /** Selected files the tool ACTUALLY mutated (≥1 mutant) — report this as the run's true scope,\n   * never the merely-requested set. */\n  mutatedFiles: string[]\n  /** Selected files the tool NEVER SAW (absent from the per-file summary) — partial under-scope.\n   * A non-empty `missing` MUST make the run inconclusive (absence-as-a-pass otherwise). */\n  missing: string[]\n}\n\n/**\n * Post-spawn partial-under-scope guard. Given the files the run was SELECTED to mutate and the\n * tool's {@link MutationSummary} (whose `files[]` carries a per-file record for every file the\n * tool SAW — even one it found no mutants in), determine which selected files were genuinely\n * mutated and which the tool never saw at all. A selected file present in the summary with zero\n * mutants is SEEN-BUT-EMPTY (benign — no mutable code); a selected file ABSENT from the summary\n * was never mutated (the partial-scope sentinel) and goes in `missing`. Paths are normalized on\n * both sides before comparison. Pure.\n */\nexport function reconcileScope(selected: string[], summary: MutationSummary): ScopeReconciliation {\n  const seen = new Set(summary.files.map((f) => normalizePath(f.path)))\n  const mutated = new Set(\n    summary.files.filter((f) => f.metrics.totalMutants > 0).map((f) => normalizePath(f.path)),\n  )\n  const sel = [...new Set(selected.map(normalizePath))].sort()\n  return {\n    mutatedFiles: sel.filter((p) => mutated.has(p)),\n    missing: sel.filter((p) => !seen.has(p)),\n  }\n}\n\n/**\n * Convert a Python source PATH to its dotted module form (`pkg/calc.py` → `pkg.calc`,\n * `pkg/__init__.py` → `pkg`). The package-relative prefix is unknown here, so this is the FULL\n * relative-path dotted form; {@link reconcileMutmutScope} matches it against mutmut's module names\n * by suffix to tolerate src-layout projects.\n */\nexport function pyPathToModule(path: string): string {\n  let p = normalizePath(path).replace(/\\.py$/, '')\n  if (p.endsWith('/__init__')) p = p.slice(0, -'/__init__'.length)\n  return p.replace(/\\//g, '.')\n}\n\n/**\n * The mutmut-specific post-spawn guard. Unlike cosmic-ray, mutmut's {@link MutationSummary} is keyed\n * by DOTTED MODULE (`pkg.calc`), not path, AND it emits NO record for a scoped file that produced\n * zero mutants (slice 0: seen-but-empty is INDISTINGUISHABLE from never-seen — Fork B2). So this is\n * deliberately CONSERVATIVE: a selected file is \"mutated\" only if some module with ≥1 mutant matches\n * its dotted form (equal, or a suffix either way — tolerating flat AND src layouts); every other\n * selected file is `missing` (⇒ the runner throws inconclusive). Some false-inconclusives, ZERO\n * false-passes (absence-is-never-a-pass). Pure.\n */\nexport function reconcileMutmutScope(\n  selectedPaths: string[],\n  summary: MutationSummary,\n): ScopeReconciliation {\n  const mutatedModules = summary.files\n    .filter((f) => f.metrics.totalMutants > 0)\n    .map((f) => normalizePath(f.path)) // mutmut paths ARE dotted modules\n  const matches = (mod: string, sel: string): boolean =>\n    mod === sel || mod.endsWith(`.${sel}`) || sel.endsWith(`.${mod}`)\n  const sel = [...new Set(selectedPaths.map(normalizePath))].sort()\n  const mutatedFiles: string[] = []\n  const missing: string[] = []\n  for (const path of sel) {\n    const mod = pyPathToModule(path)\n    if (mutatedModules.some((m) => matches(m, mod))) mutatedFiles.push(path)\n    else missing.push(path)\n  }\n  return { mutatedFiles, missing }\n}\n","/**\n * Pure mutation-report summarizer — the first slice of `@sackville-mcp/mutate`, and the one\n * with no I/O and no Stryker dependency.\n *\n * Mutation testing asks \"are the tests meaningful?\" — it perturbs the source (a `+`\n * becomes `-`, a `true` becomes `false`) and re-runs the suite; a mutant that survives is\n * a behaviour the tests do not actually pin down. Under Sackville's TDD gate the agent\n * wrote a passing test, but a passing test can still assert nothing useful — surviving\n * mutants are the catch for that, the natural complement to coverage's forgotten-assertion\n * catch (covered-but-unkilled vs added-but-uncovered).\n *\n * This module reads the **mutation-testing-elements report schema** (`schemaVersion`,\n * `files[path].mutants[].status`) that Stryker emits as `mutation-report.json`. The schema\n * is stable and decoupled from the Stryker version (ADR 0010 update 2026-06-01), so this\n * core carries no `@stryker-mutator/*` import — it is unit-tested against a committed\n * golden report. Producing a real report is a gated, injected `stryker run` (a later slice).\n *\n * Metric definitions mirror mutation-testing-elements exactly:\n *   detected   = killed + timeout\n *   undetected = survived + noCoverage\n *   covered    = detected + survived            (NoCoverage excluded — it was never run)\n *   valid      = detected + undetected\n *   invalid    = compileErrors + runtimeErrors\n *   total      = valid + invalid + ignored + pending\n *   mutationScore                 = detected / valid   (null when valid === 0)\n *   mutationScoreBasedOnCoveredCode = detected / covered (null when covered === 0)\n */\n\n/** Mutant statuses from the mutation-testing-elements schema. */\nexport type MutantStatus =\n  | 'Killed'\n  | 'Survived'\n  | 'NoCoverage'\n  | 'Timeout'\n  | 'CompileError'\n  | 'RuntimeError'\n  | 'Ignored'\n  | 'Pending'\n\nexport interface MutantPosition {\n  line: number\n  column?: number\n}\n\nexport interface Mutant {\n  id: string\n  mutatorName: string\n  status: MutantStatus\n  replacement?: string\n  location?: { start: MutantPosition; end?: MutantPosition }\n}\n\nexport interface MutationFile {\n  language?: string\n  source?: string\n  mutants: Mutant[]\n}\n\nexport interface MutationReport {\n  schemaVersion?: string\n  thresholds?: { high: number; low: number }\n  files: Record<string, MutationFile>\n}\n\nexport interface StatusCounts {\n  killed: number\n  survived: number\n  timeout: number\n  noCoverage: number\n  compileErrors: number\n  runtimeErrors: number\n  ignored: number\n  pending: number\n}\n\nexport interface MutationMetrics {\n  counts: StatusCounts\n  detected: number\n  undetected: number\n  covered: number\n  valid: number\n  invalid: number\n  totalMutants: number\n  /** detected / valid (percent); null when there are no valid mutants. */\n  mutationScore: number | null\n  /** detected / covered (percent); null when no covered mutants. */\n  mutationScoreBasedOnCoveredCode: number | null\n}\n\nexport interface FileSummary {\n  path: string\n  metrics: MutationMetrics\n}\n\n/** A surviving (or never-covered) mutant — the actionable test gap. */\nexport interface Survivor {\n  file: string\n  mutatorName: string\n  status: 'Survived' | 'NoCoverage'\n  line: number\n}\n\nexport interface MutationSummary {\n  metrics: MutationMetrics\n  files: FileSummary[]\n  /** Survived + NoCoverage mutants, sorted by file then line — what to go fix. */\n  survivors: Survivor[]\n}\n\nconst ZERO: StatusCounts = {\n  killed: 0,\n  survived: 0,\n  timeout: 0,\n  noCoverage: 0,\n  compileErrors: 0,\n  runtimeErrors: 0,\n  ignored: 0,\n  pending: 0,\n}\n\nfunction tally(mutants: Mutant[]): StatusCounts {\n  const c: StatusCounts = { ...ZERO }\n  for (const m of mutants) {\n    switch (m.status) {\n      case 'Killed':\n        c.killed++\n        break\n      case 'Survived':\n        c.survived++\n        break\n      case 'Timeout':\n        c.timeout++\n        break\n      case 'NoCoverage':\n        c.noCoverage++\n        break\n      case 'CompileError':\n        c.compileErrors++\n        break\n      case 'RuntimeError':\n        c.runtimeErrors++\n        break\n      case 'Ignored':\n        c.ignored++\n        break\n      case 'Pending':\n        c.pending++\n        break\n    }\n  }\n  return c\n}\n\nfunction metricsFrom(c: StatusCounts): MutationMetrics {\n  const detected = c.killed + c.timeout\n  const undetected = c.survived + c.noCoverage\n  const covered = detected + c.survived\n  const valid = detected + undetected\n  const invalid = c.compileErrors + c.runtimeErrors\n  const totalMutants = valid + invalid + c.ignored + c.pending\n  return {\n    counts: c,\n    detected,\n    undetected,\n    covered,\n    valid,\n    invalid,\n    totalMutants,\n    mutationScore: valid > 0 ? (detected / valid) * 100 : null,\n    mutationScoreBasedOnCoveredCode: covered > 0 ? (detected / covered) * 100 : null,\n  }\n}\n\nfunction sumCounts(a: StatusCounts, b: StatusCounts): StatusCounts {\n  return {\n    killed: a.killed + b.killed,\n    survived: a.survived + b.survived,\n    timeout: a.timeout + b.timeout,\n    noCoverage: a.noCoverage + b.noCoverage,\n    compileErrors: a.compileErrors + b.compileErrors,\n    runtimeErrors: a.runtimeErrors + b.runtimeErrors,\n    ignored: a.ignored + b.ignored,\n    pending: a.pending + b.pending,\n  }\n}\n\n/** Summarize a Stryker mutation report into aggregate + per-file metrics and the survivor list. Pure. */\nexport function summarizeMutation(report: MutationReport): MutationSummary {\n  const files: FileSummary[] = []\n  const survivors: Survivor[] = []\n  let total: StatusCounts = { ...ZERO }\n\n  for (const path of Object.keys(report.files).sort()) {\n    const file = report.files[path]\n    if (!file) continue\n    const counts = tally(file.mutants)\n    total = sumCounts(total, counts)\n    files.push({ path, metrics: metricsFrom(counts) })\n\n    for (const m of file.mutants) {\n      if (m.status === 'Survived' || m.status === 'NoCoverage') {\n        survivors.push({\n          file: path,\n          mutatorName: m.mutatorName,\n          status: m.status,\n          line: m.location?.start.line ?? 0,\n        })\n      }\n    }\n  }\n\n  survivors.sort((a, b) => (a.file < b.file ? -1 : a.file > b.file ? 1 : a.line - b.line))\n\n  return { metrics: metricsFrom(total), files, survivors }\n}\n","/**\n * The gated, diff-scoped mutation run — the live half of `@sackville-mcp/mutate`. It **spawns**\n * Stryker (`stryker run`, an injected subprocess like flake's `vitest` and coverage's\n * `vitest related`), then reads the JSON report Stryker writes and feeds it to the pure\n * {@link summarizeMutation}.\n *\n * Per ADR 0010 (+ its 2026-06-01 spike update):\n * 1. **It runs code** — and a mutation run is *expensive* (the suite re-runs per mutant) —\n *    so it sits behind the house paired deny-by-default operator gate (`allowRun` +\n *    `allowedRoots` allowlist, load-bearing on its own, + a wall-clock cap). All\n *    operator-set; no caller input self-authorizes.\n * 2. **Stryker is NOT a dependency of this package.** A real mutation run is slow and\n *    non-deterministic, so it never runs in `pnpm gate`. The `stryker` invocation is the\n *    injected {@link MutationRunner} (the bin spawns the operator's local Stryker); the\n *    engine owns the gate, argv, report plumbing, and summary, and is unit-tested with a\n *    fake runner.\n * 3. **Diff-scoped.** `mutateFiles` (the changed source files) become Stryker's `--mutate`\n *    glob list, and `--incremental` reuses Stryker's cache — so a change mutates only what\n *    it touched, not the whole tree.\n */\n\nimport { execFile } from 'node:child_process'\nimport {\n  cpSync,\n  existsSync,\n  mkdtempSync,\n  readdirSync,\n  readFileSync,\n  rmSync,\n  writeFileSync,\n} from 'node:fs'\nimport { tmpdir } from 'node:os'\nimport { join, resolve } from 'node:path'\nimport {\n  cosmicModulePathRoots,\n  mutmutDoNotMutate,\n  mutmutPathsToMutate,\n  planMutmutScope,\n  synthesizeScopedCosmicRayConfig,\n  synthesizeScopedMutmutPyproject,\n} from './config.js'\nimport { parseCosmicRayDump } from './cosmic-ray.js'\nimport { parseMutmutResults } from './mutmut.js'\nimport { reconcileMutmutScope, reconcileScope, selectMutationScope } from './scope.js'\nimport { type MutationReport, type MutationSummary, summarizeMutation } from './summarize.js'\n\n/** The zero-mutant summary returned by a pre-spawn noop (folds to no-signal ⇒ inconclusive). */\nfunction emptyMutationSummary(): MutationSummary {\n  return summarizeMutation({ files: {} })\n}\n\n/** Read a file, or undefined if it is absent (a missing base config is not an error). */\nfunction readFileIfExists(path: string): string | undefined {\n  try {\n    return readFileSync(path, 'utf8')\n  } catch {\n    return undefined\n  }\n}\n\n/** Directories never copied into the mutmut sandbox (heavy / irrelevant / the sticky mutants cache). */\nconst SANDBOX_EXCLUDE =\n  /(?:^|\\/)(?:node_modules|\\.git|\\.venv|venv|__pycache__|mutants|\\.mutmut-cache|dist|\\.tox)(?:\\/|$)/\n\n/** Recursively list the `.py` files under each owned root, repo-relative (FS default for runMutmut). */\nfunction defaultListSources(ownedRoots: string[], projectRoot: string): string[] {\n  const out: string[] = []\n  for (const root of ownedRoots) {\n    const abs = join(projectRoot, root)\n    let entries: string[]\n    try {\n      entries = readdirSync(abs, { recursive: true }) as string[]\n    } catch {\n      continue // a declared root that is a single file or absent — skip (selectMutationScope handles files)\n    }\n    for (const rel of entries) {\n      const p = rel.replace(/\\\\/g, '/')\n      if (p.endsWith('.py') && !SANDBOX_EXCLUDE.test(p))\n        out.push(`${root}/${p}`.replace(/\\/+/g, '/'))\n    }\n  }\n  return out\n}\n\n/** Copy a project into a fresh sandbox dir, excluding heavy dirs + the sticky `mutants/` cache. */\nfunction copyProjectInto(from: string, to: string): void {\n  cpSync(from, to, {\n    recursive: true,\n    filter: (src) => !SANDBOX_EXCLUDE.test(src.slice(from.length).replace(/\\\\/g, '/')),\n  })\n}\n\n/** Thrown when the paired operator gate denies a run. */\nexport class MutateGateError extends Error {\n  constructor(message: string) {\n    super(message)\n    this.name = 'MutateGateError'\n    // Brand as a gate DENIAL (ADR 0013 Addendum, milestone 5c): the run-driving\n    // `@sackville-mcp/verify` reads this global-registry symbol via `isGateDenial` to map a\n    // denial to `skipReason:'gate-not-set'` (never `errored`) WITHOUT importing engine\n    // code. The `Symbol.for` key string is the cross-package contract.\n    ;(this as unknown as Record<symbol, unknown>)[Symbol.for('sackville.gate-denial')] = true\n  }\n}\n\nexport interface RunMutationConfig {\n  /** The project to run Stryker in. */\n  projectRoot: string\n  /** OPERATOR allowlist of roots the runner may execute in. Load-bearing even with allowRun. */\n  allowedRoots: string[]\n  /** OPERATOR opt-in to actually run mutation testing. Deny-by-default. */\n  allowRun: boolean\n  /** Wall-clock cap (ms) passed to the runner. */\n  timeoutMs?: number\n}\n\nexport interface RunMutationInput {\n  /**\n   * Changed source files to scope mutation to. Stryker → `--mutate`; the Python tools → a synthesized\n   * scoped config (cosmic-ray `module-path` list / mutmut `paths_to_mutate`). `undefined` ⇒ the\n   * project default (whole project, today's behavior); a supplied list scopes the run, and a selection\n   * that resolves to no mutable in-tree `.py` is a pre-spawn noop (`ran:false`, never a spawn).\n   */\n  mutateFiles?: string[]\n  /** Reuse Stryker's incremental cache (`--incremental`) — faster re-runs. */\n  incremental?: boolean\n  /** cosmic-ray config path (relative to projectRoot). Default `cosmic-ray.toml`. */\n  configPath?: string\n  /**\n   * OPTIONAL operator source roots the diff scope is confined to (Fork C). A changed `.py` outside\n   * them is `unmatched` (report-gap), never scoped. Default: the tool config's declared source tree\n   * (cosmic-ray `module-path`).\n   */\n  ownedRoots?: string[]\n}\n\n/** Injected command runner — executes `stryker <argv>` and yields its exit status. */\nexport type MutationRunner = (\n  argv: string[],\n  opts: { cwd: string; timeoutMs?: number },\n) => Promise<{ exitCode: number; stdout: string; stderr: string }>\n\nexport interface RunMutationResult {\n  ran: boolean\n  exitCode: number\n  /** Files mutation was scoped to (empty ⇒ the project's configured set). */\n  scopedFiles: string[]\n  /** Which mutation tool produced the summary. */\n  tool?: 'stryker' | 'mutmut' | 'cosmic-ray'\n  /**\n   * The on-disk JSON report path (Stryker). Optional: the Python tools (mutmut/cosmic-ray) emit\n   * their report to STDOUT, so there is no report file to surface.\n   */\n  reportPath?: string\n  summary: MutationSummary\n  /** A scope was requested but resolved to no mutable in-tree `.py` ⇒ pre-spawn noop (case (a)). */\n  scopeEmpty?: boolean\n  /** Changed `.py` files outside the owned tree / deleted — surfaced as a gap (Fork C), never scoped. */\n  unmatched?: string[]\n  /** The files the run was SELECTED to mutate (before reconciliation) — what we asked the tool for. */\n  requestedFiles?: string[]\n}\n\n/** Stryker's default JSON-report location, relative to the project root. */\nfunction defaultReportPath(projectRoot: string): string {\n  return join(projectRoot, 'reports', 'mutation', 'mutation.json')\n}\n\n/** Build the `stryker run` argv: JSON reporter, optional diff scope + incremental cache. */\nfunction runArgv(input: RunMutationInput): string[] {\n  const argv = ['run', '--reporters', 'json']\n  if (input.mutateFiles && input.mutateFiles.length > 0) {\n    argv.push('--mutate', input.mutateFiles.join(','))\n  }\n  if (input.incremental) argv.push('--incremental')\n  return argv\n}\n\n/** Spawn a local command as a subprocess, surfacing its exit code (never rejecting on non-zero). */\nfunction spawnMutationRunner(command: string): MutationRunner {\n  return (argv, opts) =>\n    new Promise((res) => {\n      execFile(\n        command,\n        argv,\n        { cwd: opts.cwd, timeout: opts.timeoutMs, maxBuffer: 64 * 1024 * 1024 },\n        (err, stdout, stderr) => {\n          const code =\n            err && typeof (err as { code?: unknown }).code === 'number'\n              ? (err as { code: number }).code\n              : err\n                ? 1\n                : 0\n          res({ exitCode: code, stdout: String(stdout), stderr: String(stderr) })\n        },\n      )\n    })\n}\n\n/** Default live runner: spawn the local `stryker` as a subprocess (used by the bin, not the gate). */\nexport const defaultStrykerRunner: MutationRunner = spawnMutationRunner('stryker')\n\n/** Default live runner: spawn the local `mutmut` as a subprocess (used by the bin, not the gate). */\nexport const defaultMutmutRunner: MutationRunner = spawnMutationRunner('mutmut')\n\n/** Default live runner: spawn the local `cosmic-ray` as a subprocess (used by the bin, not the gate). */\nexport const defaultCosmicRayRunner: MutationRunner = spawnMutationRunner('cosmic-ray')\n\nfunction assertAllowed(config: RunMutationConfig): void {\n  if (!config.allowRun) {\n    throw new MutateGateError('mutation runs are not enabled (the operator must set allowRun)')\n  }\n  const root = resolve(config.projectRoot)\n  const allowed = config.allowedRoots.map((r) => resolve(r))\n  if (!allowed.includes(root)) {\n    throw new MutateGateError(`project root ${config.projectRoot} is not in the operator allowlist`)\n  }\n}\n\n/**\n * Run mutation testing behind the operator gate and summarize the report. The actual\n * `stryker` invocation is the injected `runner` (default {@link defaultStrykerRunner}); the\n * JSON report is read from `deps.reportPath` (default: Stryker's\n * `<projectRoot>/reports/mutation/mutation.json`).\n */\nexport async function runMutation(\n  config: RunMutationConfig,\n  input: RunMutationInput,\n  deps: { runner?: MutationRunner; reportPath?: string } = {},\n): Promise<RunMutationResult> {\n  assertAllowed(config)\n\n  const runner = deps.runner ?? defaultStrykerRunner\n  const reportPath = deps.reportPath ?? defaultReportPath(config.projectRoot)\n  const argv = runArgv(input)\n\n  const { exitCode } = await runner(argv, {\n    cwd: config.projectRoot,\n    timeoutMs: config.timeoutMs,\n  })\n\n  let report: MutationReport\n  try {\n    report = JSON.parse(readFileSync(reportPath, 'utf8')) as MutationReport\n  } catch {\n    throw new Error(\n      `mutation run did not produce a JSON report at ${reportPath} (exit code ${exitCode}); ` +\n        'ensure the project enables the Stryker `json` reporter',\n    )\n  }\n\n  return {\n    ran: true,\n    exitCode,\n    scopedFiles: input.mutateFiles ?? [],\n    tool: 'stryker',\n    reportPath,\n    summary: summarizeMutation(report),\n  }\n}\n\n/**\n * Transport-completeness guard for the Python tools, mirroring the capture/HAR guards: a run that\n * produced NO mutants (an empty/failed session), or a cosmic-ray session with unexecuted/ambiguous\n * (`Pending`) mutants, is INCONCLUSIVE — it must never be reported as a clean pass\n * (absence-is-never-a-pass). Throws so the caller (verify) folds it to inconclusive.\n */\nfunction assertComplete(tool: string, summary: MutationSummary): void {\n  if (summary.metrics.totalMutants === 0) {\n    throw new Error(`${tool} produced no mutants — inconclusive (never a clean pass)`)\n  }\n  if (summary.metrics.counts.pending > 0) {\n    throw new Error(\n      `${tool} session is incomplete: ${summary.metrics.counts.pending} unexecuted/ambiguous ` +\n        'mutant(s) — inconclusive',\n    )\n  }\n}\n\n/**\n * mutmut sibling of {@link runMutation} (ADR 0010 addendum, the lightweight Python option). Spawns\n * `mutmut run` (mutate + test; a non-zero exit just means survivors exist, not an error) then reads\n * `mutmut results --all true` from STDOUT and feeds the pure {@link parseMutmutResults}. No report\n * file. (Diff-scoping is staged — mutmut 3.x scopes via its own config, not a clean CLI file list.)\n */\nexport async function runMutmut(\n  config: RunMutationConfig,\n  input: RunMutationInput,\n  deps: {\n    runner?: MutationRunner\n    /** Existence check for the selected files (FS by default; injected in tests). */\n    exists?: (path: string) => boolean\n    /** Enumerate the `.py` files under the owned roots (for `also_copy`); FS walk by default. */\n    listSourceFiles?: (ownedRoots: string[], projectRoot: string) => string[]\n    /** The fresh sandbox cwd to run in (the sticky `mutants/` cache can't leak). Default mkdtemp. */\n    sandboxDir?: string\n  } = {},\n): Promise<RunMutationResult> {\n  assertAllowed(config)\n  const runner = deps.runner ?? defaultMutmutRunner\n\n  // Whole-project (today's behavior) in projectRoot when no scope is requested.\n  if (input.mutateFiles === undefined) {\n    const opts = { cwd: config.projectRoot, timeoutMs: config.timeoutMs }\n    await runner(['run'], opts)\n    const { exitCode, stdout } = await runner(['results', '--all', 'true'], opts)\n    const summary = summarizeMutation(parseMutmutResults(stdout))\n    assertComplete('mutmut', summary)\n    return { ran: true, exitCode, scopedFiles: [], tool: 'mutmut', summary }\n  }\n\n  // Diff-scoped: confine to the owned tree, then select mutable existing .py files.\n  const pyprojectPath = input.configPath ?? 'pyproject.toml'\n  const basePyproject = readFileIfExists(join(config.projectRoot, pyprojectPath)) ?? ''\n  const ownedRoots = input.ownedRoots ?? mutmutPathsToMutate(basePyproject)\n  const exists = deps.exists ?? ((p: string) => existsSync(join(config.projectRoot, p)))\n  const { files, unmatched } = selectMutationScope(input.mutateFiles, ownedRoots, exists)\n  const unmatchedOut = unmatched.length > 0 ? unmatched : undefined\n\n  // Case (a): nothing mutable in-tree remains — DO NOT spawn (noop).\n  if (files.length === 0) {\n    return {\n      ran: false,\n      exitCode: 0,\n      scopedFiles: [],\n      tool: 'mutmut',\n      summary: emptyMutationSummary(),\n      scopeEmpty: true,\n      unmatched: unmatchedOut,\n      requestedFiles: [],\n    }\n  }\n\n  // Plan the scope: paths_to_mutate = selected files; also_copy = the rest of the source tree so\n  // unscoped tests still import (slice 0); strip a colliding inherited do_not_mutate glob.\n  const listSources = deps.listSourceFiles ?? defaultListSources\n  const allSources = listSources(ownedRoots, config.projectRoot)\n  const plan = planMutmutScope(files, allSources, mutmutDoNotMutate(basePyproject))\n  const scopedPyproject = synthesizeScopedMutmutPyproject(basePyproject, plan)\n\n  // Fresh sandbox cwd (the mutants/ cache is sticky), with the scoped pyproject written over the copy.\n  const sandbox = deps.sandboxDir ?? mkdtempSync(join(tmpdir(), 'sackville-mutmut-'))\n  copyProjectInto(config.projectRoot, sandbox)\n  writeFileSync(join(sandbox, 'pyproject.toml'), scopedPyproject)\n\n  const opts = { cwd: sandbox, timeoutMs: config.timeoutMs }\n  await runner(['run'], opts)\n  const { exitCode, stdout } = await runner(['results', '--all', 'true'], opts)\n  const summary = summarizeMutation(parseMutmutResults(stdout))\n  // A broken scoped baseline yields \"not checked\" ⇒ Pending ⇒ assertComplete throws (slice 0): this\n  // IS the baseline-smoke gate. Total-zero is likewise inconclusive (case b).\n  assertComplete('mutmut', summary)\n  // Case (c): mutmut emits NO record for a 0-mutant selected file (Fork B2), so a selected file with\n  // no matching mutated module was never mutated ⇒ inconclusive (conservative; never a false pass).\n  const { mutatedFiles, missing } = reconcileMutmutScope(files, summary)\n  if (missing.length > 0) {\n    throw new Error(\n      `mutmut under-scoped: ${missing.join(', ')} selected but produced no mutants — inconclusive`,\n    )\n  }\n  return {\n    ran: true,\n    exitCode,\n    scopedFiles: mutatedFiles,\n    tool: 'mutmut',\n    summary,\n    requestedFiles: files,\n    unmatched: unmatchedOut,\n  }\n}\n\n/**\n * cosmic-ray sibling of {@link runMutation} (ADR 0010 addendum, the PRIMARY Python tool — its dump\n * carries real file:line:operator, so survivors are actionable). Drives the three-step workflow\n * against an operator-authored config (`input.configPath`, default `cosmic-ray.toml` — it carries\n * the project's test-command + module scope) over a throwaway session DB: `init` → `exec` → `dump`,\n * reading the `dump` JSON-lines from STDOUT and feeding the pure {@link parseCosmicRayDump}. The\n * {@link assertComplete} guard makes an empty or partially-executed session inconclusive, never a\n * clean pass. (Diff-scoping by synthesizing the per-run config from `mutateFiles` is staged.)\n */\nexport async function runCosmicRay(\n  config: RunMutationConfig,\n  input: RunMutationInput,\n  deps: {\n    runner?: MutationRunner\n    sessionDir?: string\n    /** Existence check for the selected files (FS by default; injected in tests). */\n    exists?: (path: string) => boolean\n    /** Scoped config filename written into projectRoot (relative). Default `.sackville-cosmic.toml`. */\n    scopedConfigName?: string\n  } = {},\n): Promise<RunMutationResult> {\n  assertAllowed(config)\n  const runner = deps.runner ?? defaultCosmicRayRunner\n  const opts = { cwd: config.projectRoot, timeoutMs: config.timeoutMs }\n  const configPath = input.configPath ?? 'cosmic-ray.toml'\n  const sessionDir = deps.sessionDir ?? mkdtempSync(join(tmpdir(), 'sackville-mutate-'))\n  const session = join(sessionDir, 'session.sqlite')\n\n  // Whole-project (today's behavior) when no scope is requested.\n  if (input.mutateFiles === undefined) {\n    await runner(['init', configPath, session], opts)\n    const exec = await runner(['exec', configPath, session], opts)\n    const { stdout } = await runner(['dump', session], opts)\n    const summary = summarizeMutation(parseCosmicRayDump(stdout))\n    assertComplete('cosmic-ray', summary)\n    return { ran: true, exitCode: exec.exitCode, scopedFiles: [], tool: 'cosmic-ray', summary }\n  }\n\n  // Diff-scoped: confine the changed files to the owned source tree, then select mutable existing .py.\n  const baseToml = readFileSync(join(config.projectRoot, configPath), 'utf8')\n  const ownedRoots = input.ownedRoots ?? cosmicModulePathRoots(baseToml)\n  const exists = deps.exists ?? ((p: string) => existsSync(join(config.projectRoot, p)))\n  const { files, unmatched } = selectMutationScope(input.mutateFiles, ownedRoots, exists)\n  const unmatchedOut = unmatched.length > 0 ? unmatched : undefined\n\n  // Case (a): a scope was requested but nothing mutable in-tree remains — DO NOT spawn (noop).\n  if (files.length === 0) {\n    return {\n      ran: false,\n      exitCode: 0,\n      scopedFiles: [],\n      tool: 'cosmic-ray',\n      summary: emptyMutationSummary(),\n      scopeEmpty: true,\n      unmatched: unmatchedOut,\n      requestedFiles: [],\n    }\n  }\n\n  // Synthesize a scoped config (module-path = selected files, excluded-modules reconciled). It must\n  // live in projectRoot so its RELATIVE module-path resolves there (cosmic-ray then reports relative\n  // module_path keys, which reconcileScope compares against the selected files directly).\n  const scoped = synthesizeScopedCosmicRayConfig(baseToml, files)\n  const scopedName = deps.scopedConfigName ?? '.sackville-cosmic.toml'\n  const scopedAbs = join(config.projectRoot, scopedName)\n  writeFileSync(scopedAbs, scoped.toml)\n  try {\n    await runner(['init', scopedName, session], opts)\n    const exec = await runner(['exec', scopedName, session], opts)\n    const { stdout } = await runner(['dump', session], opts)\n    const summary = summarizeMutation(parseCosmicRayDump(stdout))\n    assertComplete('cosmic-ray', summary) // case (b): total-zero / pending ⇒ inconclusive\n    // Case (c): a selected file the tool never SAW was silently never mutated ⇒ inconclusive.\n    const { mutatedFiles, missing } = reconcileScope(files, summary)\n    if (missing.length > 0) {\n      throw new Error(\n        `cosmic-ray under-scoped: ${missing.join(', ')} selected but never mutated — inconclusive`,\n      )\n    }\n    // Case (d): clean scoped run — report what was GENUINELY mutated, not what was requested.\n    return {\n      ran: true,\n      exitCode: exec.exitCode,\n      scopedFiles: mutatedFiles,\n      tool: 'cosmic-ray',\n      summary,\n      requestedFiles: files,\n      unmatched: unmatchedOut,\n    }\n  } finally {\n    rmSync(scopedAbs, { force: true })\n  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Scoping a subset breaks the\n *   baseline unless the rest of the source tree is `also_copy`'d so unscoped tests still import; an\n *   inherited `do_not_mutate` glob matching a selected file is stripped (blocker #3, mutmut form).\n *\n * Both emitters are PURE (TOML in → TOML out via `smol-toml`). They reduce SPURIOUS inconclusives by\n * reconciling exclusions up front; the load-bearing under-scope guarantee is the POST-SPAWN\n * {@link reconcileScope} guard in the runner, which folds any genuinely-unmutated selected file to\n * inconclusive regardless of why (absence-is-never-a-pass).\n */\n\nimport { parse, stringify } from 'smol-toml'\n\n/** Thrown when a scoped config cannot be safely synthesized (empty scope, missing base table, etc.). */\nexport class ScopeEmitError extends Error {\n  constructor(message: string) {\n    super(message)\n    this.name = 'ScopeEmitError'\n  }\n}\n\n/** Normalize a path to a comparable repo-relative POSIX form (backslashes → `/`, drop a leading `./`). */\nfunction normalizePath(p: string): string {\n  return p.replace(/\\\\/g, '/').replace(/^\\.\\//, '')\n}\n\n/** Dedupe + normalize + sort, the canonical scope form used everywhere. */\nfunction canonicalize(paths: string[]): string[] {\n  return [...new Set(paths.map(normalizePath))].sort()\n}\n\n/**\n * Translate a Python `fnmatch` pattern to an anchored RegExp. Mirrors `fnmatch.translate`: a star →\n * `.*` (crosses `/`, unlike shell glob — so a `star + /strutil.py` glob matches `pkg/strutil.py`),\n * `?` → any one char, `[seq]`/`[!seq]` → char class, everything else escaped. This is the matcher\n * cosmic-ray's `excluded-modules` and mutmut's `do_not_mutate` both use (the latter via\n * `fnmatch.fnmatch` in `Config.should_ignore_for_mutation`).\n */\nfunction fnmatchToRegExp(pattern: string): RegExp {\n  let re = ''\n  let i = 0\n  const n = pattern.length\n  while (i < n) {\n    const c = pattern[i++]\n    if (c === '*') {\n      re += '.*'\n    } else if (c === '?') {\n      re += '.'\n    } else if (c === '[') {\n      let j = i\n      if (j < n && (pattern[j] === '!' || pattern[j] === ']')) j++\n      while (j < n && pattern[j] !== ']') j++\n      if (j >= n) {\n        re += '\\\\[' // unterminated class → literal '['\n      } else {\n        let stuff = pattern.slice(i, j).replace(/\\\\/g, '\\\\\\\\')\n        i = j + 1\n        if (stuff.startsWith('!')) stuff = `^${stuff.slice(1)}`\n        else if (stuff.startsWith('^')) stuff = `\\\\${stuff}`\n        re += `[${stuff}]`\n      }\n    } else {\n      re += (c ?? '').replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\$&')\n    }\n  }\n  return new RegExp(`^(?:${re})$`, 's')\n}\n\n/** True if an exclusion entry (exact path or fnmatch glob) matches any of the selected files. */\nfunction exclusionCollides(entry: string, selected: string[]): boolean {\n  const norm = normalizePath(entry)\n  if (selected.includes(norm)) return true // exact path\n  const re = fnmatchToRegExp(norm)\n  return selected.some((f) => re.test(f))\n}\n\n/**\n * The operator's declared source tree, read from a cosmic-ray base config's `module-path` (a single\n * string or a list). Used as the default `ownedRoots` to confine the diff scope (Fork C): a changed\n * `.py` outside this tree is `unmatched` (report-gap), never silently scoped. Pure.\n */\nexport function cosmicModulePathRoots(baseToml: string): string[] {\n  const data = parse(baseToml) as Record<string, unknown>\n  const cr = data['cosmic-ray']\n  if (!cr || typeof cr !== 'object') return []\n  const mp = (cr as Record<string, unknown>)['module-path']\n  if (typeof mp === 'string') return [normalizePath(mp)]\n  if (Array.isArray(mp)) return mp.map((x) => normalizePath(String(x)))\n  return []\n}\n\nexport interface ScopedCosmicRayConfig {\n  /** The synthesized per-run `cosmic-ray.toml` text. */\n  toml: string\n  /** The selected file list written to `module-path` (canonical form). */\n  modulePath: string[]\n  /** Inherited `excluded-modules` entries removed because they would subtract a selected file. */\n  strippedExclusions: string[]\n}\n\n/**\n * Synthesize a per-run cosmic-ray config from a base config + the selected files. Overrides\n * `module-path` to the canonical selected FILE LIST and reconciles `excluded-modules`: any entry\n * (exact or fnmatch glob) that matches a selected file is stripped (it would otherwise silently\n * subtract that file — blocker #3); non-colliding entries are preserved. All other keys/tables\n * (`timeout`, `test-command`, `[cosmic-ray.distributor]`, …) are preserved verbatim. Pure.\n */\nexport function synthesizeScopedCosmicRayConfig(\n  baseToml: string,\n  selectedFiles: string[],\n): ScopedCosmicRayConfig {\n  const selected = canonicalize(selectedFiles)\n  if (selected.length === 0) {\n    throw new ScopeEmitError('cannot synthesize a scoped cosmic-ray config for an empty selection')\n  }\n  const data = parse(baseToml) as Record<string, unknown>\n  const cr = data['cosmic-ray']\n  if (cr === undefined || typeof cr !== 'object') {\n    throw new ScopeEmitError('base config has no [cosmic-ray] table')\n  }\n  const table = cr as Record<string, unknown>\n  table['module-path'] = selected\n\n  const strippedExclusions: string[] = []\n  const inherited = Array.isArray(table['excluded-modules'])\n    ? (table['excluded-modules'] as unknown[]).map(String)\n    : []\n  const kept = inherited.filter((entry) => {\n    if (exclusionCollides(entry, selected)) {\n      strippedExclusions.push(entry)\n      return false\n    }\n    return true\n  })\n  table['excluded-modules'] = kept\n\n  return { toml: stringify(data), modulePath: selected, strippedExclusions }\n}\n\n/** The `[tool.mutmut]` table of a pyproject (empty when absent / unparseable-as-table). */\nfunction mutmutTable(basePyproject: string): Record<string, unknown> {\n  if (!basePyproject.trim()) return {}\n  const data = parse(basePyproject) as Record<string, unknown>\n  const tool = data.tool\n  if (!tool || typeof tool !== 'object') return {}\n  const m = (tool as Record<string, unknown>).mutmut\n  return m && typeof m === 'object' ? (m as Record<string, unknown>) : {}\n}\n\n/** The operator's `[tool.mutmut] paths_to_mutate` — the default `ownedRoots` for a scoped mutmut run. */\nexport function mutmutPathsToMutate(basePyproject: string): string[] {\n  const v = mutmutTable(basePyproject).paths_to_mutate\n  return Array.isArray(v) ? v.map((x) => normalizePath(String(x))) : []\n}\n\n/** The operator's inherited `[tool.mutmut] do_not_mutate` globs (reconciled against the scope). */\nexport function mutmutDoNotMutate(basePyproject: string): string[] {\n  const v = mutmutTable(basePyproject).do_not_mutate\n  return Array.isArray(v) ? v.map(String) : []\n}\n\nexport interface MutmutScopePlan {\n  /** The selected files written to `paths_to_mutate` (canonical form). */\n  pathsToMutate: string[]\n  /** Sibling source files to `also_copy` so unscoped tests still import (source tree minus scope). */\n  alsoCopy: string[]\n  /** Inherited `do_not_mutate` globs preserved (those that do NOT collide with the scope). */\n  doNotMutate: string[]\n  /** Inherited `do_not_mutate` globs removed because they would exclude a selected file (blocker #3). */\n  strippedDoNotMutate: string[]\n}\n\n/**\n * Plan a scoped mutmut run. `paths_to_mutate` = the selected files; `also_copy` = every other source\n * file in `allSourceFiles` (so a test importing an unscoped sibling module still resolves in mutmut's\n * `mutants/` sandbox — verified necessary in slice 0). An inherited `do_not_mutate` glob that matches\n * a selected file is stripped (it would otherwise exclude a file we deliberately scoped). Pure given\n * `allSourceFiles` (the runner derives it by walking the owned roots).\n */\nexport function planMutmutScope(\n  selectedFiles: string[],\n  allSourceFiles: string[],\n  inheritedDoNotMutate: string[] = [],\n): MutmutScopePlan {\n  const pathsToMutate = canonicalize(selectedFiles)\n  if (pathsToMutate.length === 0) {\n    throw new ScopeEmitError('cannot plan a scoped mutmut run for an empty selection')\n  }\n  const scope = new Set(pathsToMutate)\n  const alsoCopy = canonicalize(allSourceFiles).filter((f) => !scope.has(f))\n\n  const strippedDoNotMutate: string[] = []\n  const doNotMutate = inheritedDoNotMutate.filter((entry) => {\n    if (exclusionCollides(entry, pathsToMutate)) {\n      strippedDoNotMutate.push(entry)\n      return false\n    }\n    return true\n  })\n  return { pathsToMutate, alsoCopy, doNotMutate, strippedDoNotMutate }\n}\n\n/**\n * Render a `pyproject.toml` for a scoped mutmut run: merge the {@link MutmutScopePlan}'s\n * `paths_to_mutate`/`also_copy` (+ reconciled `do_not_mutate`) into the base pyproject's\n * `[tool.mutmut]` table (Fork F: only slice-0-verified keys), preserving every other section and any\n * other verified `[tool.mutmut]` key the operator set (e.g. `pytest_add_cli_args`). An empty\n * `do_not_mutate` is omitted entirely. Pure.\n */\nexport function synthesizeScopedMutmutPyproject(\n  basePyproject: string,\n  plan: MutmutScopePlan,\n): string {\n  const data = (basePyproject.trim() ? parse(basePyproject) : {}) as Record<string, unknown>\n  const tool = (data.tool && typeof data.tool === 'object' ? data.tool : {}) as Record<\n    string,\n    unknown\n  >\n  const mutmut = (tool.mutmut && typeof tool.mutmut === 'object' ? tool.mutmut : {}) as Record<\n    string,\n    unknown\n  >\n  mutmut.paths_to_mutate = plan.pathsToMutate\n  mutmut.also_copy = plan.alsoCopy\n  if (plan.doNotMutate.length > 0) mutmut.do_not_mutate = plan.doNotMutate\n  else delete mutmut.do_not_mutate\n  tool.mutmut = mutmut\n  data.tool = tool\n  return stringify(data)\n}\n","/**\n * cosmic-ray adapter (a Python mutation-testing tool) — converts `cosmic-ray dump <session.sqlite>`\n * JSON-lines into the mutation-testing-elements {@link MutationReport} that {@link summarizeMutation}\n * already consumes, so the summarizer is reused unchanged across Stryker (JS), mutmut, and cosmic-ray.\n *\n * Unlike mutmut, cosmic-ray's dump carries the REAL source path + line + operator per mutant, so its\n * survivors are actionable (file:line:operator). Each dump line is a JSON array\n * `[work_item, work_result | null]` (captured from cosmic-ray 8.4.6 — see\n * `test/fixtures/cosmic-ray-dump.jsonl`):\n *\n *   - `work_item.mutations[]` — one entry per mutation in the job (single-mutation jobs in practice);\n *     each has `module_path` (the file key), `operator_name` (the mutator), and `start_pos: [line, col]`.\n *   - `work_result` — `{ worker_outcome, test_outcome? }`, or `null` when the job has not been executed.\n *\n * Status mapping (cosmic-ray → mutation-testing-elements), chosen to never overstate the score and to\n * fold ambiguity to a neutral `Pending` (never `Survived`/`Killed`):\n *   - `work_result === null`               → Pending (not yet executed)\n *   - worker_outcome `normal` + test_outcome `killed`/`survived` → Killed / Survived\n *   - worker_outcome `normal` + test_outcome `incompetent`       → RuntimeError (the mutant broke the run)\n *   - worker_outcome `no_test`             → NoCoverage (no test exercised the mutation)\n *   - worker_outcome `skipped`             → Ignored\n *   - worker_outcome `exception`/`abnormal`→ RuntimeError (invalid — excluded from the score)\n *   - worker_outcome `timeout`             → Timeout\n *   - anything else / missing test_outcome → Pending (ambiguity ⇒ neutral, never a phantom survivor)\n */\n\nimport type { Mutant, MutantStatus, MutationFile, MutationReport } from './summarize.js'\n\ninterface CosmicMutation {\n  module_path?: string\n  operator_name?: string\n  start_pos?: [number, number] | { line?: number; column?: number }\n}\ninterface CosmicWorkItem {\n  mutations?: CosmicMutation[]\n}\ninterface CosmicWorkResult {\n  worker_outcome?: string\n  test_outcome?: string | null\n}\n\n/** worker_outcome (other than `normal`) → status. `normal` defers to test_outcome. */\nconst WORKER_STATUS: Record<string, MutantStatus> = {\n  no_test: 'NoCoverage',\n  skipped: 'Ignored',\n  exception: 'RuntimeError',\n  abnormal: 'RuntimeError',\n  timeout: 'Timeout',\n}\n/** test_outcome (when worker_outcome === 'normal') → status. */\nconst TEST_STATUS: Record<string, MutantStatus> = {\n  killed: 'Killed',\n  survived: 'Survived',\n  incompetent: 'RuntimeError',\n}\n\nfunction statusOf(result: CosmicWorkResult | null): MutantStatus {\n  if (result === null) return 'Pending' // not yet executed\n  const worker = result.worker_outcome\n  if (worker === 'normal') return TEST_STATUS[result.test_outcome ?? ''] ?? 'Pending'\n  return (worker !== undefined && WORKER_STATUS[worker]) || 'Pending'\n}\n\nfunction lineColOf(\n  pos: CosmicMutation['start_pos'],\n): { line: number; column?: number } | undefined {\n  if (Array.isArray(pos)) return { line: pos[0], column: pos[1] }\n  if (pos && typeof pos.line === 'number') return { line: pos.line, column: pos.column }\n  return undefined\n}\n\n/** Parse `cosmic-ray dump <session.sqlite>` JSON-lines into a mutation-testing-elements report. Pure. */\nexport function parseCosmicRayDump(jsonl: string): MutationReport {\n  const files: Record<string, MutationFile> = {}\n  let index = 0\n  for (const raw of jsonl.split(/\\r?\\n/)) {\n    const line = raw.trim()\n    if (!line) continue\n    let parsed: [CosmicWorkItem, CosmicWorkResult | null]\n    try {\n      parsed = JSON.parse(line) as [CosmicWorkItem, CosmicWorkResult | null]\n    } catch {\n      continue // a non-JSON line (e.g. a stray log) is skipped, never a phantom mutant\n    }\n    const [workItem, workResult] = parsed\n    const mutation = workItem?.mutations?.[0]\n    const path = mutation?.module_path\n    if (!path) continue\n    const status = statusOf(workResult ?? null)\n    const loc = lineColOf(mutation.start_pos)\n    const mutant: Mutant = {\n      id: `${path}:${index}`,\n      mutatorName: mutation.operator_name ?? 'unknown',\n      status,\n    }\n    if (loc) mutant.location = { start: loc }\n    const entry = files[path] ?? { language: 'python', mutants: [] }\n    entry.mutants.push(mutant)\n    files[path] = entry\n    index++\n  }\n  return { files }\n}\n","/**\n * mutmut adapter (the Python mutation-testing tool) — converts `mutmut results --all true`\n * output into the mutation-testing-elements {@link MutationReport} that {@link summarizeMutation}\n * already consumes, so the summarizer is reused unchanged across Stryker (JS) and mutmut (Python).\n *\n * mutmut 3.x has no native mutation-testing-elements / JSON-per-mutant report; its richest\n * machine-readable per-mutant output is `mutmut results --all true`, one line per mutant:\n *\n *     calc.x_add__mutmut_1: killed\n *     calc.x_sub__mutmut_1: survived\n *     calc.x_mul__mutmut_1: no tests\n *\n * (Captured from mutmut 3.5.0 — see `test/fixtures/mutmut-results.txt`.) The mutant name is\n * `<dotted module>.x_<function>__mutmut_<n>`, so we group mutants by their module as the \"file\"\n * key (mutmut does not surface a source path or line here — `line` is 0, `mutatorName` is the\n * mutant name, the best identifier available).\n *\n * Status vocabulary mapping (mutmut → mutation-testing-elements), chosen to never overstate the\n * score: `suspicious` (the suite behaved oddly — not a confirmed kill) maps to `Survived` so it\n * surfaces as a gap; `segfault` maps to `RuntimeError` (invalid, excluded from the score); an\n * unrecognized status maps to `Pending` (neutral — excluded from `valid`, not a survivor).\n */\n\nimport type { MutantStatus, MutationFile, MutationReport } from './summarize.js'\n\nconst MUTMUT_STATUS: Record<string, MutantStatus> = {\n  killed: 'Killed',\n  survived: 'Survived',\n  'no tests': 'NoCoverage',\n  timeout: 'Timeout',\n  suspicious: 'Survived',\n  skipped: 'Ignored',\n  segfault: 'RuntimeError',\n}\n\n/** The module portion of a mutmut mutant name (`pkg.mod.x_fn__mutmut_3` → `pkg.mod`). */\nfunction moduleOf(name: string): string {\n  const m = /^(.*)\\.x_.+__mutmut_\\d+$/.exec(name)\n  if (m?.[1]) return m[1]\n  const dot = name.lastIndexOf('.')\n  return dot > 0 ? name.slice(0, dot) : name\n}\n\n/** Parse `mutmut results --all true` text into a mutation-testing-elements report. Pure. */\nexport function parseMutmutResults(text: string): MutationReport {\n  const files: Record<string, MutationFile> = {}\n  for (const raw of text.split(/\\r?\\n/)) {\n    const line = raw.trim()\n    if (!line) continue\n    const idx = line.indexOf(':')\n    if (idx === -1) continue\n    const name = line.slice(0, idx).trim()\n    if (!name) continue\n    const statusText = line\n      .slice(idx + 1)\n      .trim()\n      .toLowerCase()\n    const status = MUTMUT_STATUS[statusText] ?? 'Pending'\n    const file = moduleOf(name)\n    const entry = files[file] ?? { mutants: [] }\n    entry.mutants.push({ id: name, mutatorName: name, status })\n    files[file] = entry\n  }\n  return { files }\n}\n","/**\n * Pure scope-selection + post-spawn reconciliation primitives for Python mutation diff-scoping\n * (ADR 0010 addendum 2). The config EMITTERS (cosmic-ray TOML / mutmut pyproject) and the runner\n * wiring are STAGED pending slice-0 tool-fact capture; these two functions are the load-bearing,\n * tool-agnostic SAFETY core and ship first (pure, fixture-tested, no real tool in `pnpm gate`):\n *\n * - {@link selectMutationScope} mirrors coverage's `selectPytestScope` (incl. its INJECTED\n *   existence predicate): turn the changed-file list into the set of mutable, existing, in-tree\n *   `.py` files to scope a mutation run to, surfacing everything else as `unmatched` (report-gap;\n *   never silently folded into the scope).\n * - {@link reconcileScope} is the POST-SPAWN partial-under-scope guard (the design's load-bearing\n *   correction): the existing `assertComplete` only catches TOTAL-zero mutants, so it is blind to\n *   a run that mutated only a SUBSET of the selected files — a clean score for files that were\n *   never mutated, i.e. absence-as-a-pass. reconcileScope reports which selected files the tool\n *   actually mutated and which it NEVER SAW; the (staged) runner throws ⇒ inconclusive on any\n *   never-seen selected file.\n */\n\nimport type { MutationSummary } from './summarize.js'\n\n/** Normalize a path to a comparable repo-relative POSIX form (backslashes → `/`, drop a leading `./`). */\nfunction normalizePath(p: string): string {\n  return p.replace(/\\\\/g, '/').replace(/^\\.\\//, '')\n}\n\nexport interface MutationScope {\n  /** Mutable, existing, in-tree `.py` files to scope the run to (repo-relative, normalized, deduped, sorted). */\n  files: string[]\n  /** Changed `.py` files that are out-of-tree, deleted, or otherwise unplaceable — surfaced as a\n   * gap (report-gap), NEVER silently folded into `files` (that would be absence-as-a-pass). */\n  unmatched: string[]\n}\n\n/**\n * Derive the mutation scope from the changed files. A changed file is selected only when it is a\n * `.py` file, lives under one of the operator's `ownedRoots`, AND exists on disk (`exists`,\n * injected — FS by default in the runner, faked in tests, mirroring `selectPytestScope`'s\n * `testExists`). A `.py` file that is out-of-tree or non-existent (deleted/renamed/typo) is\n * `unmatched`, never scoped. Non-`.py` files are irrelevant to mutation and dropped. Pure given\n * `exists`. Whole-project fallback is NOT decided here — it is the caller's (`mutateFiles ===\n * undefined`) or the cosmic-ray emitter's (`no-scope` on the base config) concern.\n */\nexport function selectMutationScope(\n  mutateFiles: string[],\n  ownedRoots: string[],\n  exists: (path: string) => boolean,\n): MutationScope {\n  const roots = ownedRoots.map(normalizePath)\n  const underRoot = (p: string): boolean => roots.some((r) => p === r || p.startsWith(`${r}/`))\n  const files = new Set<string>()\n  const unmatched = new Set<string>()\n  for (const raw of mutateFiles) {\n    const p = normalizePath(raw)\n    if (!p.endsWith('.py')) continue // not a Python source file — irrelevant to mutation\n    if (!underRoot(p) || !exists(p)) {\n      unmatched.add(p) // out-of-tree, deleted, renamed, or typo'd — a gap, never scoped\n      continue\n    }\n    files.add(p)\n  }\n  return { files: [...files].sort(), unmatched: [...unmatched].sort() }\n}\n\nexport interface ScopeReconciliation {\n  /** Selected files the tool ACTUALLY mutated (≥1 mutant) — report this as the run's true scope,\n   * never the merely-requested set. */\n  mutatedFiles: string[]\n  /** Selected files the tool NEVER SAW (absent from the per-file summary) — partial under-scope.\n   * A non-empty `missing` MUST make the run inconclusive (absence-as-a-pass otherwise). */\n  missing: string[]\n}\n\n/**\n * Post-spawn partial-under-scope guard. Given the files the run was SELECTED to mutate and the\n * tool's {@link MutationSummary} (whose `files[]` carries a per-file record for every file the\n * tool SAW — even one it found no mutants in), determine which selected files were genuinely\n * mutated and which the tool never saw at all. A selected file present in the summary with zero\n * mutants is SEEN-BUT-EMPTY (benign — no mutable code); a selected file ABSENT from the summary\n * was never mutated (the partial-scope sentinel) and goes in `missing`. Paths are normalized on\n * both sides before comparison. Pure.\n */\nexport function reconcileScope(selected: string[], summary: MutationSummary): ScopeReconciliation {\n  const seen = new Set(summary.files.map((f) => normalizePath(f.path)))\n  const mutated = new Set(\n    summary.files.filter((f) => f.metrics.totalMutants > 0).map((f) => normalizePath(f.path)),\n  )\n  const sel = [...new Set(selected.map(normalizePath))].sort()\n  return {\n    mutatedFiles: sel.filter((p) => mutated.has(p)),\n    missing: sel.filter((p) => !seen.has(p)),\n  }\n}\n\n/**\n * Convert a Python source PATH to its dotted module form (`pkg/calc.py` → `pkg.calc`,\n * `pkg/__init__.py` → `pkg`). The package-relative prefix is unknown here, so this is the FULL\n * relative-path dotted form; {@link reconcileMutmutScope} matches it against mutmut's module names\n * by suffix to tolerate src-layout projects.\n */\nexport function pyPathToModule(path: string): string {\n  let p = normalizePath(path).replace(/\\.py$/, '')\n  if (p.endsWith('/__init__')) p = p.slice(0, -'/__init__'.length)\n  return p.replace(/\\//g, '.')\n}\n\n/**\n * The mutmut-specific post-spawn guard. Unlike cosmic-ray, mutmut's {@link MutationSummary} is keyed\n * by DOTTED MODULE (`pkg.calc`), not path, AND it emits NO record for a scoped file that produced\n * zero mutants (slice 0: seen-but-empty is INDISTINGUISHABLE from never-seen — Fork B2). So this is\n * deliberately CONSERVATIVE: a selected file is \"mutated\" only if some module with ≥1 mutant matches\n * its dotted form (equal, or a suffix either way — tolerating flat AND src layouts); every other\n * selected file is `missing` (⇒ the runner throws inconclusive). Some false-inconclusives, ZERO\n * false-passes (absence-is-never-a-pass). Pure.\n */\nexport function reconcileMutmutScope(\n  selectedPaths: string[],\n  summary: MutationSummary,\n): ScopeReconciliation {\n  const mutatedModules = summary.files\n    .filter((f) => f.metrics.totalMutants > 0)\n    .map((f) => normalizePath(f.path)) // mutmut paths ARE dotted modules\n  const matches = (mod: string, sel: string): boolean =>\n    mod === sel || mod.endsWith(`.${sel}`) || sel.endsWith(`.${mod}`)\n  const sel = [...new Set(selectedPaths.map(normalizePath))].sort()\n  const mutatedFiles: string[] = []\n  const missing: string[] = []\n  for (const path of sel) {\n    const mod = pyPathToModule(path)\n    if (mutatedModules.some((m) => matches(m, mod))) mutatedFiles.push(path)\n    else missing.push(path)\n  }\n  return { mutatedFiles, missing }\n}\n","/**\n * Pure mutation-report summarizer — the first slice of `@sackville-mcp/mutate`, and the one\n * with no I/O and no Stryker dependency.\n *\n * Mutation testing asks \"are the tests meaningful?\" — it perturbs the source (a `+`\n * becomes `-`, a `true` becomes `false`) and re-runs the suite; a mutant that survives is\n * a behaviour the tests do not actually pin down. Under Sackville's TDD gate the agent\n * wrote a passing test, but a passing test can still assert nothing useful — surviving\n * mutants are the catch for that, the natural complement to coverage's forgotten-assertion\n * catch (covered-but-unkilled vs added-but-uncovered).\n *\n * This module reads the **mutation-testing-elements report schema** (`schemaVersion`,\n * `files[path].mutants[].status`) that Stryker emits as `mutation-report.json`. The schema\n * is stable and decoupled from the Stryker version (ADR 0010 update 2026-06-01), so this\n * core carries no `@stryker-mutator/*` import — it is unit-tested against a committed\n * golden report. Producing a real report is a gated, injected `stryker run` (a later slice).\n *\n * Metric definitions mirror mutation-testing-elements exactly:\n *   detected   = killed + timeout\n *   undetected = survived + noCoverage\n *   covered    = detected + survived            (NoCoverage excluded — it was never run)\n *   valid      = detected + undetected\n *   invalid    = compileErrors + runtimeErrors\n *   total      = valid + invalid + ignored + pending\n *   mutationScore                 = detected / valid   (null when valid === 0)\n *   mutationScoreBasedOnCoveredCode = detected / covered (null when covered === 0)\n */\n\n/** Mutant statuses from the mutation-testing-elements schema. */\nexport type MutantStatus =\n  | 'Killed'\n  | 'Survived'\n  | 'NoCoverage'\n  | 'Timeout'\n  | 'CompileError'\n  | 'RuntimeError'\n  | 'Ignored'\n  | 'Pending'\n\nexport interface MutantPosition {\n  line: number\n  column?: number\n}\n\nexport interface Mutant {\n  id: string\n  mutatorName: string\n  status: MutantStatus\n  replacement?: string\n  location?: { start: MutantPosition; end?: MutantPosition }\n}\n\nexport interface MutationFile {\n  language?: string\n  source?: string\n  mutants: Mutant[]\n}\n\nexport interface MutationReport {\n  schemaVersion?: string\n  thresholds?: { high: number; low: number }\n  files: Record<string, MutationFile>\n}\n\nexport interface StatusCounts {\n  killed: number\n  survived: number\n  timeout: number\n  noCoverage: number\n  compileErrors: number\n  runtimeErrors: number\n  ignored: number\n  pending: number\n}\n\nexport interface MutationMetrics {\n  counts: StatusCounts\n  detected: number\n  undetected: number\n  covered: number\n  valid: number\n  invalid: number\n  totalMutants: number\n  /** detected / valid (percent); null when there are no valid mutants. */\n  mutationScore: number | null\n  /** detected / covered (percent); null when no covered mutants. */\n  mutationScoreBasedOnCoveredCode: number | null\n}\n\nexport interface FileSummary {\n  path: string\n  metrics: MutationMetrics\n}\n\n/** A surviving (or never-covered) mutant — the actionable test gap. */\nexport interface Survivor {\n  file: string\n  mutatorName: string\n  status: 'Survived' | 'NoCoverage'\n  line: number\n}\n\nexport interface MutationSummary {\n  metrics: MutationMetrics\n  files: FileSummary[]\n  /** Survived + NoCoverage mutants, sorted by file then line — what to go fix. */\n  survivors: Survivor[]\n}\n\nconst ZERO: StatusCounts = {\n  killed: 0,\n  survived: 0,\n  timeout: 0,\n  noCoverage: 0,\n  compileErrors: 0,\n  runtimeErrors: 0,\n  ignored: 0,\n  pending: 0,\n}\n\nfunction tally(mutants: Mutant[]): StatusCounts {\n  const c: StatusCounts = { ...ZERO }\n  for (const m of mutants) {\n    switch (m.status) {\n      case 'Killed':\n        c.killed++\n        break\n      case 'Survived':\n        c.survived++\n        break\n      case 'Timeout':\n        c.timeout++\n        break\n      case 'NoCoverage':\n        c.noCoverage++\n        break\n      case 'CompileError':\n        c.compileErrors++\n        break\n      case 'RuntimeError':\n        c.runtimeErrors++\n        break\n      case 'Ignored':\n        c.ignored++\n        break\n      case 'Pending':\n        c.pending++\n        break\n    }\n  }\n  return c\n}\n\nfunction metricsFrom(c: StatusCounts): MutationMetrics {\n  const detected = c.killed + c.timeout\n  const undetected = c.survived + c.noCoverage\n  const covered = detected + c.survived\n  const valid = detected + undetected\n  const invalid = c.compileErrors + c.runtimeErrors\n  const totalMutants = valid + invalid + c.ignored + c.pending\n  return {\n    counts: c,\n    detected,\n    undetected,\n    covered,\n    valid,\n    invalid,\n    totalMutants,\n    mutationScore: valid > 0 ? (detected / valid) * 100 : null,\n    mutationScoreBasedOnCoveredCode: covered > 0 ? (detected / covered) * 100 : null,\n  }\n}\n\nfunction sumCounts(a: StatusCounts, b: StatusCounts): StatusCounts {\n  return {\n    killed: a.killed + b.killed,\n    survived: a.survived + b.survived,\n    timeout: a.timeout + b.timeout,\n    noCoverage: a.noCoverage + b.noCoverage,\n    compileErrors: a.compileErrors + b.compileErrors,\n    runtimeErrors: a.runtimeErrors + b.runtimeErrors,\n    ignored: a.ignored + b.ignored,\n    pending: a.pending + b.pending,\n  }\n}\n\n/** Summarize a Stryker mutation report into aggregate + per-file metrics and the survivor list. Pure. */\nexport function summarizeMutation(report: MutationReport): MutationSummary {\n  const files: FileSummary[] = []\n  const survivors: Survivor[] = []\n  let total: StatusCounts = { ...ZERO }\n\n  for (const path of Object.keys(report.files).sort()) {\n    const file = report.files[path]\n    if (!file) continue\n    const counts = tally(file.mutants)\n    total = sumCounts(total, counts)\n    files.push({ path, metrics: metricsFrom(counts) })\n\n    for (const m of file.mutants) {\n      if (m.status === 'Survived' || m.status === 'NoCoverage') {\n        survivors.push({\n          file: path,\n          mutatorName: m.mutatorName,\n          status: m.status,\n          line: m.location?.start.line ?? 0,\n        })\n      }\n    }\n  }\n\n  survivors.sort((a, b) => (a.file < b.file ? -1 : a.file > b.file ? 1 : a.line - b.line))\n\n  return { metrics: metricsFrom(total), files, survivors }\n}\n","/**\n * The gated, diff-scoped mutation run — the live half of `@sackville-mcp/mutate`. It **spawns**\n * Stryker (`stryker run`, an injected subprocess like flake's `vitest` and coverage's\n * `vitest related`), then reads the JSON report Stryker writes and feeds it to the pure\n * {@link summarizeMutation}.\n *\n * Per ADR 0010 (+ its 2026-06-01 spike update):\n * 1. **It runs code** — and a mutation run is *expensive* (the suite re-runs per mutant) —\n *    so it sits behind the house paired deny-by-default operator gate (`allowRun` +\n *    `allowedRoots` allowlist, load-bearing on its own, + a wall-clock cap). All\n *    operator-set; no caller input self-authorizes.\n * 2. **Stryker is NOT a dependency of this package.** A real mutation run is slow and\n *    non-deterministic, so it never runs in `pnpm gate`. The `stryker` invocation is the\n *    injected {@link MutationRunner} (the bin spawns the operator's local Stryker); the\n *    engine owns the gate, argv, report plumbing, and summary, and is unit-tested with a\n *    fake runner.\n * 3. **Diff-scoped.** `mutateFiles` (the changed source files) become Stryker's `--mutate`\n *    glob list, and `--incremental` reuses Stryker's cache — so a change mutates only what\n *    it touched, not the whole tree.\n */\n\nimport {\n  cpSync,\n  existsSync,\n  mkdtempSync,\n  readdirSync,\n  readFileSync,\n  rmSync,\n  writeFileSync,\n} from 'node:fs'\nimport { tmpdir } from 'node:os'\nimport { join, resolve } from 'node:path'\nimport { type SpawnedRunner, spawnRunner } from '@sackville-mcp/spawn'\nimport {\n  cosmicModulePathRoots,\n  mutmutDoNotMutate,\n  mutmutPathsToMutate,\n  planMutmutScope,\n  synthesizeScopedCosmicRayConfig,\n  synthesizeScopedMutmutPyproject,\n} from './config.js'\nimport { parseCosmicRayDump } from './cosmic-ray.js'\nimport { parseMutmutResults } from './mutmut.js'\nimport { reconcileMutmutScope, reconcileScope, selectMutationScope } from './scope.js'\nimport { type MutationReport, type MutationSummary, summarizeMutation } from './summarize.js'\n\n/** The zero-mutant summary returned by a pre-spawn noop (folds to no-signal ⇒ inconclusive). */\nfunction emptyMutationSummary(): MutationSummary {\n  return summarizeMutation({ files: {} })\n}\n\n/** Read a file, or undefined if it is absent (a missing base config is not an error). */\nfunction readFileIfExists(path: string): string | undefined {\n  try {\n    return readFileSync(path, 'utf8')\n  } catch {\n    return undefined\n  }\n}\n\n/** Directories never copied into the mutmut sandbox (heavy / irrelevant / the sticky mutants cache). */\nconst SANDBOX_EXCLUDE =\n  /(?:^|\\/)(?:node_modules|\\.git|\\.venv|venv|__pycache__|mutants|\\.mutmut-cache|dist|\\.tox)(?:\\/|$)/\n\n/** Recursively list the `.py` files under each owned root, repo-relative (FS default for runMutmut). */\nfunction defaultListSources(ownedRoots: string[], projectRoot: string): string[] {\n  const out: string[] = []\n  for (const root of ownedRoots) {\n    const abs = join(projectRoot, root)\n    let entries: string[]\n    try {\n      entries = readdirSync(abs, { recursive: true }) as string[]\n    } catch {\n      continue // a declared root that is a single file or absent — skip (selectMutationScope handles files)\n    }\n    for (const rel of entries) {\n      const p = rel.replace(/\\\\/g, '/')\n      if (p.endsWith('.py') && !SANDBOX_EXCLUDE.test(p))\n        out.push(`${root}/${p}`.replace(/\\/+/g, '/'))\n    }\n  }\n  return out\n}\n\n/** Copy a project into a fresh sandbox dir, excluding heavy dirs + the sticky `mutants/` cache. */\nfunction copyProjectInto(from: string, to: string): void {\n  cpSync(from, to, {\n    recursive: true,\n    filter: (src) => !SANDBOX_EXCLUDE.test(src.slice(from.length).replace(/\\\\/g, '/')),\n  })\n}\n\n/** Thrown when the paired operator gate denies a run. */\nexport class MutateGateError extends Error {\n  constructor(message: string) {\n    super(message)\n    this.name = 'MutateGateError'\n    // Brand as a gate DENIAL (ADR 0013 Addendum, milestone 5c): the run-driving\n    // `@sackville-mcp/verify` reads this global-registry symbol via `isGateDenial` to map a\n    // denial to `skipReason:'gate-not-set'` (never `errored`) WITHOUT importing engine\n    // code. The `Symbol.for` key string is the cross-package contract.\n    ;(this as unknown as Record<symbol, unknown>)[Symbol.for('sackville.gate-denial')] = true\n  }\n}\n\nexport interface RunMutationConfig {\n  /** The project to run Stryker in. */\n  projectRoot: string\n  /** OPERATOR allowlist of roots the runner may execute in. Load-bearing even with allowRun. */\n  allowedRoots: string[]\n  /** OPERATOR opt-in to actually run mutation testing. Deny-by-default. */\n  allowRun: boolean\n  /** Wall-clock cap (ms) passed to the runner. */\n  timeoutMs?: number\n}\n\nexport interface RunMutationInput {\n  /**\n   * Changed source files to scope mutation to. Stryker → `--mutate`; the Python tools → a synthesized\n   * scoped config (cosmic-ray `module-path` list / mutmut `paths_to_mutate`). `undefined` ⇒ the\n   * project default (whole project, today's behavior); a supplied list scopes the run, and a selection\n   * that resolves to no mutable in-tree `.py` is a pre-spawn noop (`ran:false`, never a spawn).\n   */\n  mutateFiles?: string[]\n  /** Reuse Stryker's incremental cache (`--incremental`) — faster re-runs. */\n  incremental?: boolean\n  /** cosmic-ray config path (relative to projectRoot). Default `cosmic-ray.toml`. */\n  configPath?: string\n  /**\n   * OPTIONAL operator source roots the diff scope is confined to (Fork C). A changed `.py` outside\n   * them is `unmatched` (report-gap), never scoped. Default: the tool config's declared source tree\n   * (cosmic-ray `module-path`).\n   */\n  ownedRoots?: string[]\n}\n\n/** Injected command runner — executes `stryker <argv>` and yields its exit status. */\nexport type MutationRunner = SpawnedRunner\n\nexport interface RunMutationResult {\n  ran: boolean\n  exitCode: number\n  /** Files mutation was scoped to (empty ⇒ the project's configured set). */\n  scopedFiles: string[]\n  /** Which mutation tool produced the summary. */\n  tool?: 'stryker' | 'mutmut' | 'cosmic-ray'\n  /**\n   * The on-disk JSON report path (Stryker). Optional: the Python tools (mutmut/cosmic-ray) emit\n   * their report to STDOUT, so there is no report file to surface.\n   */\n  reportPath?: string\n  summary: MutationSummary\n  /** A scope was requested but resolved to no mutable in-tree `.py` ⇒ pre-spawn noop (case (a)). */\n  scopeEmpty?: boolean\n  /** Changed `.py` files outside the owned tree / deleted — surfaced as a gap (Fork C), never scoped. */\n  unmatched?: string[]\n  /** The files the run was SELECTED to mutate (before reconciliation) — what we asked the tool for. */\n  requestedFiles?: string[]\n}\n\n/** Stryker's default JSON-report location, relative to the project root. */\nfunction defaultReportPath(projectRoot: string): string {\n  return join(projectRoot, 'reports', 'mutation', 'mutation.json')\n}\n\n/** Build the `stryker run` argv: JSON reporter, optional diff scope + incremental cache. */\nfunction runArgv(input: RunMutationInput): string[] {\n  const argv = ['run', '--reporters', 'json']\n  if (input.mutateFiles && input.mutateFiles.length > 0) {\n    argv.push('--mutate', input.mutateFiles.join(','))\n  }\n  if (input.incremental) argv.push('--incremental')\n  return argv\n}\n\n/** Default live runner: spawn the local `stryker` as a subprocess (used by the bin, not the gate). */\nexport const defaultStrykerRunner: MutationRunner = spawnRunner('stryker')\n\n/** Default live runner: spawn the local `mutmut` as a subprocess (used by the bin, not the gate). */\nexport const defaultMutmutRunner: MutationRunner = spawnRunner('mutmut')\n\n/** Default live runner: spawn the local `cosmic-ray` as a subprocess (used by the bin, not the gate). */\nexport const defaultCosmicRayRunner: MutationRunner = spawnRunner('cosmic-ray')\n\nfunction assertAllowed(config: RunMutationConfig): void {\n  if (!config.allowRun) {\n    throw new MutateGateError('mutation runs are not enabled (the operator must set allowRun)')\n  }\n  const root = resolve(config.projectRoot)\n  const allowed = config.allowedRoots.map((r) => resolve(r))\n  if (!allowed.includes(root)) {\n    throw new MutateGateError(`project root ${config.projectRoot} is not in the operator allowlist`)\n  }\n}\n\n/**\n * Run mutation testing behind the operator gate and summarize the report. The actual\n * `stryker` invocation is the injected `runner` (default {@link defaultStrykerRunner}); the\n * JSON report is read from `deps.reportPath` (default: Stryker's\n * `<projectRoot>/reports/mutation/mutation.json`).\n */\nexport async function runMutation(\n  config: RunMutationConfig,\n  input: RunMutationInput,\n  deps: { runner?: MutationRunner; reportPath?: string } = {},\n): Promise<RunMutationResult> {\n  assertAllowed(config)\n\n  const runner = deps.runner ?? defaultStrykerRunner\n  const reportPath = deps.reportPath ?? defaultReportPath(config.projectRoot)\n  const argv = runArgv(input)\n\n  const { exitCode } = await runner(argv, {\n    cwd: config.projectRoot,\n    timeoutMs: config.timeoutMs,\n  })\n\n  let report: MutationReport\n  try {\n    report = JSON.parse(readFileSync(reportPath, 'utf8')) as MutationReport\n  } catch {\n    throw new Error(\n      `mutation run did not produce a JSON report at ${reportPath} (exit code ${exitCode}); ` +\n        'ensure the project enables the Stryker `json` reporter',\n    )\n  }\n\n  return {\n    ran: true,\n    exitCode,\n    scopedFiles: input.mutateFiles ?? [],\n    tool: 'stryker',\n    reportPath,\n    summary: summarizeMutation(report),\n  }\n}\n\n/**\n * Transport-completeness guard for the Python tools, mirroring the capture/HAR guards: a run that\n * produced NO mutants (an empty/failed session), or a cosmic-ray session with unexecuted/ambiguous\n * (`Pending`) mutants, is INCONCLUSIVE — it must never be reported as a clean pass\n * (absence-is-never-a-pass). Throws so the caller (verify) folds it to inconclusive.\n */\nfunction assertComplete(tool: string, summary: MutationSummary): void {\n  if (summary.metrics.totalMutants === 0) {\n    throw new Error(`${tool} produced no mutants — inconclusive (never a clean pass)`)\n  }\n  if (summary.metrics.counts.pending > 0) {\n    throw new Error(\n      `${tool} session is incomplete: ${summary.metrics.counts.pending} unexecuted/ambiguous ` +\n        'mutant(s) — inconclusive',\n    )\n  }\n}\n\n/**\n * mutmut sibling of {@link runMutation} (ADR 0010 addendum, the lightweight Python option). Spawns\n * `mutmut run` (mutate + test; a non-zero exit just means survivors exist, not an error) then reads\n * `mutmut results --all true` from STDOUT and feeds the pure {@link parseMutmutResults}. No report\n * file. (Diff-scoping is staged — mutmut 3.x scopes via its own config, not a clean CLI file list.)\n */\nexport async function runMutmut(\n  config: RunMutationConfig,\n  input: RunMutationInput,\n  deps: {\n    runner?: MutationRunner\n    /** Existence check for the selected files (FS by default; injected in tests). */\n    exists?: (path: string) => boolean\n    /** Enumerate the `.py` files under the owned roots (for `also_copy`); FS walk by default. */\n    listSourceFiles?: (ownedRoots: string[], projectRoot: string) => string[]\n    /** The fresh sandbox cwd to run in (the sticky `mutants/` cache can't leak). Default mkdtemp. */\n    sandboxDir?: string\n  } = {},\n): Promise<RunMutationResult> {\n  assertAllowed(config)\n  const runner = deps.runner ?? defaultMutmutRunner\n\n  // Whole-project (today's behavior) in projectRoot when no scope is requested.\n  if (input.mutateFiles === undefined) {\n    const opts = { cwd: config.projectRoot, timeoutMs: config.timeoutMs }\n    await runner(['run'], opts)\n    const { exitCode, stdout } = await runner(['results', '--all', 'true'], opts)\n    const summary = summarizeMutation(parseMutmutResults(stdout))\n    assertComplete('mutmut', summary)\n    return { ran: true, exitCode, scopedFiles: [], tool: 'mutmut', summary }\n  }\n\n  // Diff-scoped: confine to the owned tree, then select mutable existing .py files.\n  const pyprojectPath = input.configPath ?? 'pyproject.toml'\n  const basePyproject = readFileIfExists(join(config.projectRoot, pyprojectPath)) ?? ''\n  const ownedRoots = input.ownedRoots ?? mutmutPathsToMutate(basePyproject)\n  const exists = deps.exists ?? ((p: string) => existsSync(join(config.projectRoot, p)))\n  const { files, unmatched } = selectMutationScope(input.mutateFiles, ownedRoots, exists)\n  const unmatchedOut = unmatched.length > 0 ? unmatched : undefined\n\n  // Case (a): nothing mutable in-tree remains — DO NOT spawn (noop).\n  if (files.length === 0) {\n    return {\n      ran: false,\n      exitCode: 0,\n      scopedFiles: [],\n      tool: 'mutmut',\n      summary: emptyMutationSummary(),\n      scopeEmpty: true,\n      unmatched: unmatchedOut,\n      requestedFiles: [],\n    }\n  }\n\n  // Plan the scope: paths_to_mutate = selected files; also_copy = the rest of the source tree so\n  // unscoped tests still import (slice 0); strip a colliding inherited do_not_mutate glob.\n  const listSources = deps.listSourceFiles ?? defaultListSources\n  const allSources = listSources(ownedRoots, config.projectRoot)\n  const plan = planMutmutScope(files, allSources, mutmutDoNotMutate(basePyproject))\n  const scopedPyproject = synthesizeScopedMutmutPyproject(basePyproject, plan)\n\n  // Fresh sandbox cwd (the mutants/ cache is sticky), with the scoped pyproject written over the copy.\n  const sandbox = deps.sandboxDir ?? mkdtempSync(join(tmpdir(), 'sackville-mutmut-'))\n  copyProjectInto(config.projectRoot, sandbox)\n  writeFileSync(join(sandbox, 'pyproject.toml'), scopedPyproject)\n\n  const opts = { cwd: sandbox, timeoutMs: config.timeoutMs }\n  await runner(['run'], opts)\n  const { exitCode, stdout } = await runner(['results', '--all', 'true'], opts)\n  const summary = summarizeMutation(parseMutmutResults(stdout))\n  // A broken scoped baseline yields \"not checked\" ⇒ Pending ⇒ assertComplete throws (slice 0): this\n  // IS the baseline-smoke gate. Total-zero is likewise inconclusive (case b).\n  assertComplete('mutmut', summary)\n  // Case (c): mutmut emits NO record for a 0-mutant selected file (Fork B2), so a selected file with\n  // no matching mutated module was never mutated ⇒ inconclusive (conservative; never a false pass).\n  const { mutatedFiles, missing } = reconcileMutmutScope(files, summary)\n  if (missing.length > 0) {\n    throw new Error(\n      `mutmut under-scoped: ${missing.join(', ')} selected but produced no mutants — inconclusive`,\n    )\n  }\n  return {\n    ran: true,\n    exitCode,\n    scopedFiles: mutatedFiles,\n    tool: 'mutmut',\n    summary,\n    requestedFiles: files,\n    unmatched: unmatchedOut,\n  }\n}\n\n/**\n * cosmic-ray sibling of {@link runMutation} (ADR 0010 addendum, the PRIMARY Python tool — its dump\n * carries real file:line:operator, so survivors are actionable). Drives the three-step workflow\n * against an operator-authored config (`input.configPath`, default `cosmic-ray.toml` — it carries\n * the project's test-command + module scope) over a throwaway session DB: `init` → `exec` → `dump`,\n * reading the `dump` JSON-lines from STDOUT and feeding the pure {@link parseCosmicRayDump}. The\n * {@link assertComplete} guard makes an empty or partially-executed session inconclusive, never a\n * clean pass. (Diff-scoping by synthesizing the per-run config from `mutateFiles` is staged.)\n */\nexport async function runCosmicRay(\n  config: RunMutationConfig,\n  input: RunMutationInput,\n  deps: {\n    runner?: MutationRunner\n    sessionDir?: string\n    /** Existence check for the selected files (FS by default; injected in tests). */\n    exists?: (path: string) => boolean\n    /** Scoped config filename written into projectRoot (relative). Default `.sackville-cosmic.toml`. */\n    scopedConfigName?: string\n  } = {},\n): Promise<RunMutationResult> {\n  assertAllowed(config)\n  const runner = deps.runner ?? defaultCosmicRayRunner\n  const opts = { cwd: config.projectRoot, timeoutMs: config.timeoutMs }\n  const configPath = input.configPath ?? 'cosmic-ray.toml'\n  const sessionDir = deps.sessionDir ?? mkdtempSync(join(tmpdir(), 'sackville-mutate-'))\n  const session = join(sessionDir, 'session.sqlite')\n\n  // Whole-project (today's behavior) when no scope is requested.\n  if (input.mutateFiles === undefined) {\n    await runner(['init', configPath, session], opts)\n    const exec = await runner(['exec', configPath, session], opts)\n    const { stdout } = await runner(['dump', session], opts)\n    const summary = summarizeMutation(parseCosmicRayDump(stdout))\n    assertComplete('cosmic-ray', summary)\n    return { ran: true, exitCode: exec.exitCode, scopedFiles: [], tool: 'cosmic-ray', summary }\n  }\n\n  // Diff-scoped: confine the changed files to the owned source tree, then select mutable existing .py.\n  const baseToml = readFileSync(join(config.projectRoot, configPath), 'utf8')\n  const ownedRoots = input.ownedRoots ?? cosmicModulePathRoots(baseToml)\n  const exists = deps.exists ?? ((p: string) => existsSync(join(config.projectRoot, p)))\n  const { files, unmatched } = selectMutationScope(input.mutateFiles, ownedRoots, exists)\n  const unmatchedOut = unmatched.length > 0 ? unmatched : undefined\n\n  // Case (a): a scope was requested but nothing mutable in-tree remains — DO NOT spawn (noop).\n  if (files.length === 0) {\n    return {\n      ran: false,\n      exitCode: 0,\n      scopedFiles: [],\n      tool: 'cosmic-ray',\n      summary: emptyMutationSummary(),\n      scopeEmpty: true,\n      unmatched: unmatchedOut,\n      requestedFiles: [],\n    }\n  }\n\n  // Synthesize a scoped config (module-path = selected files, excluded-modules reconciled). It must\n  // live in projectRoot so its RELATIVE module-path resolves there (cosmic-ray then reports relative\n  // module_path keys, which reconcileScope compares against the selected files directly).\n  const scoped = synthesizeScopedCosmicRayConfig(baseToml, files)\n  const scopedName = deps.scopedConfigName ?? '.sackville-cosmic.toml'\n  const scopedAbs = join(config.projectRoot, scopedName)\n  writeFileSync(scopedAbs, scoped.toml)\n  try {\n    await runner(['init', scopedName, session], opts)\n    const exec = await runner(['exec', scopedName, session], opts)\n    const { stdout } = await runner(['dump', session], opts)\n    const summary = summarizeMutation(parseCosmicRayDump(stdout))\n    assertComplete('cosmic-ray', summary) // case (b): total-zero / pending ⇒ inconclusive\n    // Case (c): a selected file the tool never SAW was silently never mutated ⇒ inconclusive.\n    const { mutatedFiles, missing } = reconcileScope(files, summary)\n    if (missing.length > 0) {\n      throw new Error(\n        `cosmic-ray under-scoped: ${missing.join(', ')} selected but never mutated — inconclusive`,\n      )\n    }\n    // Case (d): clean scoped run — report what was GENUINELY mutated, not what was requested.\n    return {\n      ran: true,\n      exitCode: exec.exitCode,\n      scopedFiles: mutatedFiles,\n      tool: 'cosmic-ray',\n      summary,\n      requestedFiles: files,\n      unmatched: unmatchedOut,\n    }\n  } finally {\n    rmSync(scopedAbs, { force: true })\n  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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sackville-mcp/mutate",
-  "version": "0.0.1-alpha.3",
+  "version": "0.0.1-alpha.4",
   "type": "module",
   "license": "Apache-2.0",
   "exports": {
@@ -16,7 +16,8 @@
     "dist"
   ],
   "dependencies": {
-    "smol-toml": "^1.6.1"
+    "smol-toml": "^1.6.1",
+    "@sackville-mcp/spawn": "0.0.1-alpha.4"
   },
   "publishConfig": {
     "access": "public"